Hi Holeinone
I understand you pain, as do many other commanders

.
We have all been there, sat wondering which gun it is[where is it][where is it].. Add in the fun fact that the drop ship, gun ship and FAS had their weapon ports swapped round(load out screen glitch) made for great fun when shooting- oh that is a pulse laser.. not a multicannon... hmmm[noob]
Like others have stated, there are planned changes for the load out section with the next latch, it is going to be a huge improvement(lets hope it is even better than the sneak peak we saw).
So for now-
list your ship and we can go from there, as this will give us a great deal of information and we can thrown in some screen shots to help you out.
Basic ship 101 information:
Ships like the also the
Cobra 3 are easy- top front guns(as in just under your windshield) are class 2, bottom guns are class 1(aka under your feet).
The Viper's are the other war round- small class 1 on the top, medium class 2 on the bottom, thanks to sirroco- been a long time since i have flown one...
Click the spoiler to see some of the ships.
Cobra MK4 Top guns are class 1- there are 3 of them, front guns class 2(again under the windshield).
Ships like the FDL and Python are equally as easy- the Python -Belly gun is class 3, top front class 2, top back class 3.
FDL Belly gun class 4(yes HUGE) top 4 are class 2- simples!
When you get into things like the gun ship and Anaconda it gets a bit messy with 7 guns, but by then you will know what to do- unless a friend gave you his account
Fly safe and learn your load out.