Generally intelligence actions, especially threat are an aspect of the game you can't pass on. Intel can be more useful than diplomacy and uses fewer leaderships points.
The success you are having in the field of intelligence depends on how big a part of your Leadership you invest into spying. When you hover over intelligence slider in the technology window you will see how many spies per day you are getting. Simply do the math if it's enough to train 25-30 people to work for you at home and abroad by the time you will want to wage a war. If it doesn't, you have to invest more leadership.
What to do with your spies? During peace time and build up period for the war you probably want to work on your neutrality regardless if you want to be peaceful or not. Lowering neutrality allows you to enact some of the more strict and thus more efficient economic laws and is very desirable for every nation.
If you know you are heavily spied on and you don't need to lower your neutrality more since your laws are very strict already, you can switch to counter-intelligence. This will allow you to catch spies that work inside your borders much more easily. It's easiest to notice you're spied on when hovering over the techs you are researching. If it says spies disrupting research hurt you -1 or -2% it's fine... but if it goes up to ~10% you surely need to counter that.
Abroad during pre-war years you should work on raising threat of someone. A typical Axis member will have 10 spies raising threat of their first victim so the sum of threat and lowered neutrality allows waging a war much earlier. A typical allies member will shout loudly Axis members are evil raising their threat and pushing nations out of Axis corner back towards Allies.
The second part can be skipped as some countries though. For example Poland should invest everything into counter-intelligence since German threat and their neutrality already have good enough values. On the other hand Romania, Bulgaria or Hungary who want to jump and annex Yugoslavia before Italians do that should from day one heavily raise threat of that country and aggressively lower their own neutrality at the same time. This way a war in early 1937 is very much possible in this region and snatching Yugoslavia and Albania denying Italians from conquering it is very much possible.
The first intelligence priority of any country should be to get 10 spies (the maximum) at home. The AI does not perform counterespionage on foreign countries, so unless you are playing against humans this will be a one-time cost.
There are four possible missions for domestic intelligence.
Choosing this option will help clear out enemy spies in your country. Note that choosing other missions will not stop counterespionage efforts completely, but a focus on counterespionage will let you find and neutralize enemy spies more quickly.
Support Ruling Party
Probably the least useful of the missions, although ruling party popularity is necessary for the harsher civil laws if one is a democracy. (All countries start out with Fractured Government condition which negatively affects your national Unity. Supporting the ruling party is typically the only way to remove this effect as most countries don't have access to enough ministers of each party type which would otherwise fix Fractured Government.)
Generally the most useful mission. Lower Neutrality means lower Consumer Goods demand, and is necessary for enacting the better Conscription and Economic Laws when not at war. More importantly, it lowers the necessary Threat in order to declare war against another nation. (No Longer possible in TFH. Non major nations get a prepare for war national decision which reduces your neutrality over time for a set period of time)
Raise National Unity
Raises your National Unity. This is a slow effect, but can be useful, mostly for enacting better laws.
Press Laws will affect your domestic intelligence efforts. If you are raising your National Unity it pays to have less restrictive laws; on the other hand, more restrictive laws are better for Counterespionage. Essentially, keep the presses free to report news, as long as it's good.
If you wish to keep tabs on an enemy AI nation, the best strategy is to dump 10 spies into that nation and select the Counterespionage mission. You may take some losses early on, but sooner or later you will wipe out their domestic intelligence service. The AI will not be able to respond, as any spy that pops up will be neutralized immediately. This also makes them extremely vulnerable to the spies of your allies.
If you want to declare war against another nation, or repel other countries away from them diplomatically, use the Increase Threat mission.
Using the Disrupt National Unity mission on a country can reduce the number of Victory Points you need to defeat them, which may open up opportunities to annex them in a quick surprise attack. Don't expect it to win the war for you otherwise, however.
Having built a good reserve of spies (8-10), it's possible to send them all at once to a foreign country quickly building a strong spy network able to conduct multiple actions. But for most actions abroad, this net will be very fragile and enemy spies will quickly overwhelm player's spies. So it will be necessary to keep high leadership investment into spies (1.5-2 for major countries) to replace fallen agents.
There's an alternative to this. Placing 8-10 spies at once abroad and setting them to Counter-espionage mission will allow them to start attacking enemy defensive spies. They will quickly bring enemy counter-espionage strength to 0. Some of the attackers are likely to fall during this initial combat so replacements need to be prepared. Later, when enemy defence is very low, replacements will no longer be necessary and maintaining 10 spies in his country won't be as hard to achieve.
When enemy has no defenders left, two possibilities arise:
- Switching to a more useful mission, lowering enemy's national unity for example.
- Staying with Counter-espionage killing enemy domestic spies as soon as enemy tries to place them, keeping his counter-espionage at 0 and allowing spies from allied countries to wreck his research and production without being targeted. When enemy country's threat raises during the war and ranks of his enemies grow, this action becomes especially dangerous often leading to 30-40% research and production penalties which can cripple even a major.
Scouting and Sabotage
To choose one of these, you click on the province and chose the option from the province information window. Make use of the "scout area" and "sabotage area" missions. These intel missions have a powerful effect when used along with your main effort at breakthrough. Each mission can affect up to 7 provinces--you can slow enemy reserves from reaching the area, and speed yours through--also giving a further combat advantage in speed. You can save up enough covert points for 3 such missions at one time. It takes a while to amass 45 points--so start early.
Propaganda and You: A Strategy Guide by Green Marine is a very good writeup about how to use the intel threat mission for Germany.