It really depends on the hotel and their protocols. I have pre-paid via check for hotels by making the reservation and then calling them and asking if I can do so. Most are accommodating, but some do not deal with checks on any level.

Make your reservation as normal and then call them and ask (or vice-versa). If you are going to wait to send in the check, make sure you send in the check in plenty of time for them to receive it and deposit it and then have it clear the bank.

Of the occasions I have sent in pre-payment with a check, I make absolutely sure I have a copy of the cleared check in case there are any disputes (and, unfortunately, there was one where a night clerk swore up and down the hotel never received the check until I produced the copy).

Once you get there, they may ask for a credit card for "incidentals" but you can usually negotiate putting down $100 or so in case for those incidentals and getting the cash back when you check out.

I hope that helps.