I'm assuming that the separate bookings would be IAH-LIM-IAH and IAH-PHL-IAH.

If you really do intend to fly from LIM through to IAH without stopping for any appreciable amount of time in Houston then book it as a single ticket. If anything were to happen on the return and you didn't get to IAH in time to pick up the PHL flight you'd be hosed. It may change the fare rules and the change fees a bit but if you're pretty confident on the travel dates and times I'd just do the single ticket.

And your qualification for Silver (Congrats!) doesn't require the PHL-IAH flight, right? Because that won't be until the 2011 qualification starts.