Not quite sure what is happening, in particular don't know what yoyu mean by "only the effects work".

That aside, I'll make a number of observations:

1) Most H9 effects are mono/stereo, meaning they expect a single mono instrument or a single stereo instrument. Using two different instruments may be interesting, but probably not useful.

2) A dynamic microphone like SM58 has a very low impedance, so if it ends up in parallel with the bass it will short it out, and you may get almost nothing.

3) A dynamic microphone like SM58 has a very low output level, so unless you run it through a preamp first, it will be inaudible, or drowned in noise or both.

So, for all the above reasons, I would suggest you rethink.