If you have an external tuner, I would use that tuner and supply S-video to the capture card. Your external tuner is in a better environment (better shielding) and should, in most cases, do a better tuning job.
Also, if you send an RF signal to the HTPC, you won't get digital cable channels.
If you do go this route, you don't need to be concerned with the audio tuning features of your capture card, which can vary. On the other hand, this means you have to send audio from your set top box to your PCs sound card (or straight to the tv or stereo, which would preclude any VCR-type features for your HTPC).