Set your crossover in the Yamaha to 90 Hz and either disable the crossover on your subwoofer entirely, or set it to 200 Hz (the highest frequency). You never want to set both crossovers at the same frequency, as it would produce an artificially steep drop-off in frequency response. You need not worry about music content from 90-200 Hz being output from the sub, because the receiver is already taking that data and sending it to your regular speakers.
If you have very good front speakers, and your amplifier allows you to do so, you can set the crossover frequency lower than 90 Hz so that more low frequency bass is produced by the fronts. The THX recommended crossover point is 80 Hz, but lots of people go with 60 Hz with front tower speakers that have good bass response, and even as low as 40 Hz for playing music. For HT use where LFE can be very powerful, I'd stick with 80 Hz and use a good sub to handle everything below 80 Hz.
Which Yamaha do you have? I know the higher end models allow you to mix and match the bass frequencies between the front speakers and the sub. My RX-V2500 has "Front" - "Both" and "SWFR" settings for Bass Out. If you set the output to "Both" then the LFE data is sent to the subwoofer, but all bass content from the Left/Right/Center is sent to BOTH the Subwoofer and Fronts. Personally, I prefer the SWFR setting which sends all bass below the crossover point to the Subwoofer - but I like my sub, a lot. =)
Greg