Confusion with Engineers/upgrades

I will try to explain my confusion without confusing anyone,lol. So awhile back I wen to Tod The blaster and modified my frag canon to a level 2. I just went back to him after getting a bunch of raw materials to add more engineering upgrades. So I decided to add some overcharged upgrades. I finished 2 levels but it seemed I had to generate the upgrades 2 and 3 times. So first question–how do you know when it's complete? It seems like you can just re-generate over and over–except each time you do you use up resources. Next problem–I noticed the message just before I did the overcharged upgrade that it would over write any changes on my previous upgrades to the double shot I had done. Well it did–now my overcharged is upgraded but my previous upgrades on the doubleshot are gone. So net question–can I only upgrade 1 thing for each weapon? Next I went to try the 3rd tier for overcharged. I had the necessary resources–but it said all the lower upgrades for that type must be done–which again I thought I did. When I look at the 1st and w2nd tiers–the first has a yellow hexagon icon with a checkmark in it. The 2nd just has a yellow hexagon–no check mark–but the 3rd also has the same yellow hexagon–so totally confused what that means. Lastly the first upgrade I did previously–the double shot, now has the first level with a yellow hexagon, and the ones for level 2 and 3 are white. O know this must sound confusing as everything. Could someone shed some light on this stuff? Oh one last thing–when I go into the engineer screen it shows level 3 access for what it's worth. Thanks