It's okay to use two low frequency instruments if you want to, as long as they don't interfere with each other, and the levels are handled correctly. I'd try it first, and see how it sounds.
Low frequencies(<250Hz) take up almost half of the logarithmic frequency spectrum. So any interference between notes or instruments at those frequencies seems exaggerated.
If you feel there is notable interference, sidechain compression could be the way to go.
As an example, let's say you want the bass guitar to be the dominant sound rather than the Hammond:
Insert a compressor with sidechain capabilities on the Hammond channel. Then use an aux send to send the bass guitar into the compressor's sidechain channel. Then every time the level of the bass track reaches the threshold defined in the compressor, the Hammond will be compressed. You can adjust Ratio/Attack/Release etc to suit. If you use a multi-band compressor, you will have more control over which frequencies of the Hammond get compressed, so the rest of the Hammond sound is untouched.