If I just HAD to mix them both into the cut at once I would let the real bass (with the groove) be the main deal.
Just get it good sounding and then add the sequenced part with a hipass that allows it to be heard/felt.
You could consider moving the sequenced bassline up an octave maybe?
If it isn't tracked and still lives in MIDI I'd experiment until I found a sound that worked with the real bass.

I have been FORCED to listen to a lot of electronica and dance/club music over the last four years and I have analyzed how that stuff is mixed with the HUGE bass drum sounds.
The actual bassline has the low end rolled off at a point that is above the kick drum.
It is pretty much "implied."

It's a psychological trick, but it's possible.

One has to be the "winner" in low end though.

BTW, I do a lot of stuff that is old C&W where I'll have standup (upright ACSTC) bass and a baritone guitar as well. I had to study older recordings and it is similar to what you are talking about. The upright bass is playing simpler 1/5 alternating lines like most people associate with C&W and the baritone GTR will be playing more arpeggiated lines.
The tone of the baritone through an amp is generally such that it doesn't have a lot of low end that clashes with the upright/string bass. It is fun combination! Tricky at times.

Good luck!

Danny Brown