screw the spare David. Thats what your yearly AAA payments are for. I have had my LS400 w/o any spare for a daily driven 3 years and only had 1 flat. I waited a total of 30min and was at a local repair place. Just do an overall check every couple weeks for nails/cuts.
Also, fix a flat isn't a bad idea either like Jib said.
As for the battery location you can mount in your old cd changer location or do what I did... bolt a battery box to your spare tire well floor and fill around it with Great Stuff expanding foam. the battery box lid will seal it and for good measure throw the factory floor on top of that. By putting the battery here you benefit from mounting 50lb in a very low position on the car, much lower that the factory underhood location. Also, the battery will be at the furthest back location possible, aiding in front/rear distribution as well as increased traction from this weight being placed slightly behind the rear wheels. Your SC will handle better immidiatly after this swap.
BTW, I upgraded my battery to an optima yellow top and I never had charging/reserve issues