I've spent years figuring out this problem. The best way to do it i've found is to learn songs which feature the polyrhythms in question. I'll start with a great video by Guthrie Govan that I Looooooove for understanding odd note groupings.
Check out Steve Vai's Tempo Mental page on his website. that will give you a fantastic in-depth guide to the extremities of polyrhythms, and even a way to pratice(notating speech)
The Bone alphabet by Brian Ferneyhough is way, way out of the playability zone for the majority of players, but the extreme depth of polyrhythms listened to for a while gets your mind in the zone that it can consider polyrhythms
The Black Page by Frank Zappa is a similar piece, along with the majority of Frank Zappa's Music (but be warned, no 2 albums are the same, It's a very difficult soundscape at times)
As far as books go, the book I use is Polyrhythms:The Musician's Guide by Peter Magadinni. It takes you through playing the basic pulses of any polyrhythm up to 13:4. It also includes more complex rhythm patterns within your polyrhythms(for example a 3/4 pattern over a 4/4 pulse).
And at the risk of self promoting, I've also written a few articles on Odd Time Signatures that may help.
Hope that helps. Polyrhythms are a wonderful tool once they're natural, but until then you gotta grind it out!