I have set up 2 tracks, kick and bass, and have the bass ducking a little when the kick hits.  
 
The bass also has a lot of mid frequencies that I don't want to duck - I just want to duck the part of the bass that matches the kick frequency (to avoid the frequency clash).
 
Any suggestions how to achieve this.  I'm using Fab Filter C2.

You could clone your bass DI track. Lo-pass/high-pass them for your preference. By that I mean. Bass DI 1: 0-500Hz and bass DI 2 500-10000Hz...

Then you can sidechain your kickdrum to Bass DI 1..

Would that do?

Cloning the track would work or send to a couple of buses and use the Sonitus Multiband as crossovers on the buses. Add Pro-C to the appropriate bus. If it were SONAR Platinum, the LP MB with its new sidechain feature would work right on the bass track.

This is clearly an application for a multiband compressor like FabFilter MB, LP MB or Sonitus Multiband.
 
I would not clone tracks; this is fairly retro since the introduction of aux tracks ;-) and a hassle in case you still need to do some edits to the track
 

Oh, thats not the main reason I clone my bass DI :)

I prefer adding a tiny amount of drive from 5-600+hz. Adding drive below this frequency I feel muds up the track. Therefore I only add drive to my bass DI 2.

I add a limiter on both bass DI tracks, but with different settings. That way I can keep the sexy sub even on the high notes.

It might be retro... but is retro that bad?

:D

No need to make it more complicated than necessary. Pro-C already has what you need: a sidechain filter. Just set it up as a low-pass filter.

Multiband compression is how I do it.

One thing to watch is that the "smack” as pedal hits drumskin is a large part of what gives the initial transient of a kick drum much of its impact. That transient can include some surprisingly high frequency components. To find out what they are have a look at the kick drum's frequency plot in the eq or a meter.

Thanks for the replies and suggestions.
 
bitflipper:  I thought of using Pro-C's side chain filter, but isn't that controlling the part of the (in my case) kick that activates the compression the bass: eg, if its high-passed, then it will compress the bass less, but it will still compress all of the bass?   When actually what I need is to compress only part of the bass frequency, but not all of it.   Or did I misunderstand the Pro-C's side chain filter?  If I understood right, then Pro-MB would logically be the right tool, I can set just one band of it to control exactly which frequency range in the bass I want compressed when the kick hits.
 

Use a dynamic EQ like Pro-MB for complex tracks and busses. Use a broadband compressor with filtered sidechain for sonically-simple tracks such as kick, bass and vocals.
 
The filter determines what the sidechain sees. If you're compressing the bass using the drum track as the sidechain key, and therefore only want low frequencies to trigger the compression, then a LPF is the answer. That's going to reduce the amount of high frequencies the compressor's sidechain hears, so they'll have little or no affect on the bass compression.

https://www.youtube.com/watch?v=glRU9H37Fbo    Heres a video I made regarding something similar, although not identical.  
The technique I used here allows you to manipulate the signal you are sending to the sidechain.  Using Alloy 2 allows you to choose which part of the multiband is sidechained, the gate as well