Ok, I don't know how this is supposed to be, but from what I've understood, you're supposed to be able to get level 3 cloaking which makes you invisible.

Now, let's say I'm a Skulk. We have a few of each Upgrade Chamber, and for my first upgrade I choose cloaking. HOW do I go to level 2 cloaking? I just can't seem to be able to upgrade another level?!

Isn't that supposed to be possible??

yeah ive been wondering about those levels also

When you team have one sensor chamber you can upgrade your alien to have cloak...now when your team build up second sensor chamber you have lvl2 cloak and when they build up third you have then lvl3 cloak. if your team build up more sensor chambers it will not help anymore to get cloak better and it works same way in any upgrades