yea, totally agree - I realised about 30 mins before deadline that it was confusing and had no time to change.
You need to Press Q to throw containers into the green extractor - money earn in the resource gathering side is used to build towers and then money collected in the defence side can be used for towers or if you Time jump back using the time porter you can unlock upgrades.
There is a bunch of simplification that needs to be done and an actual tutorial - once the Jam is over I will release an update to fix those issues.
Sorry for your frustrations