Yes I would add a cap just in case the amp biases the input (unlikely) I suspect the value won't be too critical because you're not going to 'hear' the signal that's going into the EQ, but a value that provides enough low end of the lowest bin in your EQ. It is best to keep your ground 'clean' but I see no reason not to just connect it all, with a pass-through the enclosure out to your amp, your circuit inside.
With that said, what are you using to power this? Most plug in power supplies are isolated so there probably won't be trouble with ground loops - but they are also noisy - having digital switching transients going on a board, inside a shielded enclosure, where the bass signal is routed (admittedly from just one socket to another) it could pick up noise. Also many 1/4" sockets are all metal, making the enclosure signal ground, but also some DC sockets are (assuming you're using that for power input). This would connect the DC supply ground and signal ground, and if the supply isn't isolated there could be ground loops. Guitar pedals that can accept DC power supplies generally have the enclosure the same as the signal ground and many of those are pretty quiet

Best thing would be to test it. Bass -> 1/4" socket -> 1/4" socket - patch cable to amp, to give you access to the signal and ground. Connect a buffer amplifier to it via a switch, and see if you can hear a difference when the circuit is on. Effectively a 'blank' pedal that is always bypassed, but switches a circuit to 'look at' the signal.
Post a schem of what you have so far.