Something that I've been pondering lately, that probably warrants another thread, is which input do you use after an FX chain? After it's gone through some buffered effects, should you use a particular input on the amp? As well as cutting the volume, the active input usually has a lower impedance, which will affect the signal. Some of my pedals sound quite different when plugged into the active input compared to passive.
For example, my DHA VT2. If I set the gains and master volume to give an equal signal level when on and off, then move it to the active input, I get a severe volume drop when the effect is on. I'm sure this is due to impedance mismatching (low inpedance of the amp causing voltage drop at the pedal's output stage) and it confuses the hell out of me!
Once you've gone through a chain of fx, the matter of whether the source bass was active or passive may become irrelevant and you can stick to using one input on the amp. Stick an A/B box at the front of the chain for switching instruments and use some other pedal to control the volume between the 2 (if there is any). You can also get pedals like the Bassbone to take 2 basses with an adjustable volume control for each.