Is it OK to use wood sealer or putty on bad joints an gaps and then epoxy over them or should I fill gaps with something else??

Thanks in advance!

It is ok to use wood fillers as long as they don't react with the epoxy coating.
I would stay away from water baced wood fillers. I like to use a filler called Plasti bond, it is water proof.  Some other fillers like car bog  will go soft when in contact with water.