Karen,
Like you, I have a company car and a company credit card. I worry about being stopped by the police in the company car while en femme and the officer deciding to call the company for some lame reason and outing me, or worse yet, I know if I had a wreck and had to go to the hospital I know they'd call the office. But, that's a little off topic. My hotel drill is this: First of all, I stay in a place where I can park at my door and not have to walk through a lobby (Is this a motel rather than a hotel?). I don't use my company credit card. I put it on my expense account later. I check in in more-or-less androgenous mode, which would typically be girl's jeans, top, and shoes, little to no makeup, and my hair kind of fem or in a ponytail (my hair is collar bone length). Im comfortable with this for a number of reasons. I'm still recognizable by my photo I.D. and my male name credit card is not questioned. I'm pretty comfortable in androgenous mode, and I don't ruffle any feathers. This is about the best I can pull off after work. If they see me later, I've left enough clues that no one will be surprised.
I have no problem checking out en femme, and, in fact, look forward to it. It's kind of the first test of the morning. I've always been treated extremely well, and usually get a "mam" to brightem my day! I'll spend a day doing my thing, then go through the inevitable change on the drive home (makeup removing wipes work amazingly well while driving).