I posted a suggestion to the KSP forums here about the ability to switch an individual parts root option more easily to better facilitate complex alignment and ensure that docking ports would be aligned in the VAB/SPH.

I'm sure this is an issue that many of us more veteran players have run into at one point or another. It can be very difficult to align multiple docking ports for large stations across multiple trusses in such a way as to ensure that they'll dock.

The best solution is often to stick a piece in between the docks in such a way as to make sure the docks align, but to ensure this in this way it is then impossible to get the docking ports to connect to the piece in such a way as to transport it as a single unit.

I'll let the forum post speak for itself.