I've always had this problem when making songs with basslines that fall in the frequency because that is where a lot of the punchiness of a kick is in the subwoofer space. I know what you're think just sidechain it well it doesn't work as well as what I just figured out.
When putting your 808/bassline into the piano roll, cut the note short 1/4 of a step right before the next note hits. IT WORKS! I will make a video tomorrow explaining it if you don't get it...
And really this works great with any note/frequency, but it mostly makes a difference on the 40-50hz range.
This really is incredible to me. I haven't learned something this useful in a long long time...
Pics:
This is the sample I'm working with. It's the 808 from the Lex Luger Kit.

This is what a normal piano roll for me looks like when I do 808s.

This is what I will now be doing. NOTICE THE INSTRUMENT PROPERTIES TAB I TURNED THE VOLUME ADSR ON TO MAKE IT SO THE SAMPLE ONLY PLAYS WHEN THE NOTE IN THE PIANO ROLL IS THERE.

Just try it for yourselves to see the difference. I think it just creates a bigger dynamic range from the bass to the next kick because of the split second silence.