I'm going through similar issues with my setup, but I think installing/running soft-15 is a simple one time thing, run it, click the install for the 15, 25, 31 resolutions and you're done. It just adds resolutions to your registry. Then you should see all the resolutions in quickres. I think i had to restart to get them to show up in quickres.
I second the idea of a simple guide to setting it up, the thread is like 40 pages of fairly useless info to me, with a few tidbits of decent info.
You need the extra resolutions once you leave your front end and run mame. The front end isnt be able to set the resolutions on a game by game basis(i'm not sure though about atomicfe since i use mala), mame does that.
most older tv's should have some knobs on the back to let you adjust horizontal and vertical height, and shift, if not the service menu can.
***after rereading your post, I'm really not sure soft-15 is needed for a tv, its meant specifically for connecting to arcade monitors.