Since vanilla configs are balanced around having only 1 covert action at a time, this mod is totally not balanced for it. But since there's no other overhauls that make use and balance around multiple covert actions yet, we can discuss and share your config here for others to play with.

My own input:

Since the default config lets you still only have 1 action early game but more action late game. A place to start is to reduce the effectiveness of engineer speeding up the covert actions, as with 3 actions its effect is essentially tripled, lowering from 33% to 15%.

In addition, there are some covert actions that is clearly better than other covert actions in different parts of the game, by tweaking the duration we can make those covert actions as attractive as the essential ones. So stuff like increase region income which is very underwhelming throughout the game (just about as much as an average retaliation mission?) can preserve its duration, while things like reducing avatar progress or finding facility lead which is almost an auto pick every time should have its duration increased between 200% to 250%.

Recruit faction soldier/engineer/scientist/new resistance contact also have enough impact that it warrants an increase between 150% to 200% in duration.

Then there's gather supplies which is also already a pretty big time investment for the low amount of supplies it generates, it should at most increase between 50% to 100% in duration. However gather intel do provide a decent amount of intel, so it should increase in 100% to 150% in duration instead.

Rescue soldier should only need an increase between 50% to 100% in duration as it can happen early game and you need to deploy a real mission for it anyways.

Stuff like improve soldier bonds, improve combat intelligence, recover alien loot, and manufacture weapon upgrade is kind of good but you wouldn't choose them until you are stacking late game soldiers so they can have a smaller duration increase of 50% to 100%.

While new resistance orders, and research breakthrough do quickly become auto-picks when it rolls a good choice, so an increase of 150% to 200% is needed to make them a tougher choice.

Fabricate PCS should have a 100% to 150% increase due to how rare superior PCS are although they are not very crucial before the very late game.

Gain ability points should also see a 100% to 150% increase with the amount of AP it gives, which is enough for 2 normal abilities or 1 high ranking ability.

For story related covert actions, find faction should have the same amount of time taken as you need them to upgrade your max covert actions, with the following actions duration increased between 100% to 200%.