I have a separate card, primarily used by my son, but I also use it to play. My wife, his stepmom, doesn't get those bills. They come to me electronically. Wife & I keep separate finances, so it's easier for me. I'm not sure if I'm stupid by hiding in plain sight, but if she ever got that far down the paper trail, I'd be sunk anyway.

You could get a pre-paid vanilla visa & load it up with enough for all the holds, etc.
I tend not to do pre-paid rooms, just because shit happens. If you avoid pre-pay sites, just use your cc to guarantee the room & pay cash when you check out. The hotel doesn't care.

Book using a Visa Target gift card. Buy card with cash. Book hotel in SBs name if you have her real name. Ask her to check in first and put her CC for incidentals with the hotel. Go straight to the room after she's checked in.
This way nothing leads back to you.

I still remember checking into a really nice four star Hilton with a long time SB who was 30 years younger than me in Atlanta some time back. I no longer lived in Atlanta so most of the time I'd get a hotel when I'd come to town. AAR I left my luggage in the car so it was me and this young twenty something year old hottie checking into the hotel together with no luggage. They checked us, well actually they checked "ME" into the hotel and asked me how many keys I needed so I told them only one because the girl with me was only a hooker I had picked up. ROFLMFAO.

 
The guy behind the desk didn't know whether or not to laugh, shit his pants or what the fuck to do. I was literally LOLing and my SB was laughing right along too, well after she called me a "Fucking asshole" of course.  

 
I have to be honest, I understand why you married guys have to be careful, but for the rest of you, take a chill pill, No one really cares if you are renting the room just to fuck.  As long as YOU don't think you are doing anything wrong, neither will anyone else

Get a credit card and stop paper bills and set up a pin number so you can withdraw cash. I'm married as well and even though I do the finances at home I don't want to risk leaving a paper trail. My primary method of funds come from a cash advance. I pay ~$15 total on a single withdraw but its worth every penny in my opinion. I pay the CC soon after so I dont accumulate finance charges. The CC payment showing up on the bank account doesnt raise any red flags because its from the same bank. If by any chance the statement shows up at your door step say that it was a fraud