I've posted on this before. (I'm waiting for someone to post a snide remark about using the search function). I use my points for cheques; I find it's the best use of my points - your mileage may vary.

As for getting proper credit (your payment treated as if you paid in cash), it's definitely hit and miss. I'd say that 2/3s of the time I have to call Marriott to get them to correct the points for the stay.
The reason for not getting proper credit for cheques is because the person at the front desk usually inputs the credits with the wrong code so that it appears to be Bonus Bucks or some other credit that doesn't receive points. I have had desk clerks take up to 45 minutes trying to figure out how to input the cheques ... for that reason, I use the cheques well prior to checkout; usually at check in. If they are still clueless after a few minutes, I head up to my room and tell them that I'll stop back later.
Since you don't get any cash back when paying by cheque, I always pay a small amount with my MR visa.