One option is to use the subscription card in one tuner & a Free TV card in the other (the 20 pound card that gives you C4, five, five US, five Life & Sky Three) the use Mark Salloway's Media Center Tuner Priority utility to force the subscription card to be used first for all Live TV & recordings http://www.salloway.org.uk/mediacenter/util/index.htm
Hooking up the Sky box to MCE in the standard way via s-video &L/R audio with an analogue capture card like the Hauppauge WinTV PVR-150 does work very well. The picture quality isn't as good as direct DVB-S using a FloppyDTV or similar but it's pretty good for moderate sized TVs. You can substitute a Pacelink device for the IR bug for maximum channel changing reliability http://www.pacelink.co.uk/rf2link.htm