The location of the cap doesn't matter. Or, at least, it won't cause you to get no sound or incorrect performance from the volume controls. The two V-V-T diagrams you've posted on this page of the thread are basically the same in terms of how the volumes are configured and how they should work.
The Aguilar diagram up top shows ground symbols instead of actually drawing in all of the ground wires. Did you ground all the spots where the ground symbol is used? All you need to do is connect them all together (as shown by the actual wires in the Bartolini diagram).
To be honest it's a little hard to give specific help since it seems like you're changing direction and trying different things as you go. It might be easier if we can stick to one diagram and one plan and then figure it out.
Can you try the following three things and tell us what happens? I'm getting a little confused by the way you're describing what's happening.
1) Turn the neck volume all the way up and the bridge volume all the way down.
2) Turn the bridge volume all the way up, and the neck volume all the way down.
3) Turn both volumes all the way up.
Tell us what happens in each of those three and we can get a better idea of what's going on here. Once we know the volumes are set up correctly, then we can work on the tone pot if we need to.