There should be no problem with the through checking of your baggage.

There is a transit hotel at BKK airport. I've not stayed there but I beleive it's quite good and you need not go through migration/customs etc and you save the THB 500 departure tax.

There is also an Amari attached to the airport but that's after customs/migration.

Unless transit time is critical, I would not bother with either. Hop in a meter taxi (do not bother with overpriced 'limos') and stay in town at one of the many excellent value, top quality hotels that Bangkok has to offer.