The idea with this is that a special module can have two different modes. With just a little energy you can change what it does. So lets say you have a Tactical Scanning Console module on your ship. One mode it gives a bonus to attack change it over it gives a bonus to scanning instead. This would be each bonus could be on the higher end while not breaking the bank. Yes costing 5 energy to change from one to other might be a pain but it means you need to plan what you will be doing a little more.

Or just to expand on your idea have it be one module that dose 2 things. Let’s say cloak and scan for an example. Say device has 100 point 50 scan 50 cloak to start when u put it on. However you can set a percent to this device by default it starts as 50% scan, 50% cloak. By using say 5 or 10 energy you can change the percent so if you want more scan power you adjust the % bar to 75 % scans and 25% clock making the total value now read 75 scan and 25 cloak.

This type of idea needs to be as simple as it can be. Adjusting the % of the whole modules is likely to much.

Naw red, why I said only 2 abilities. Have a % bar under the item that slides left and right. 50/50 being the center point. If you want scan you go left if you want cloak you go right.
And if need be store them under a new tab called duel modules on the ship screen.