...You may have to create multiple Process Recipes (PRs) with their own absolute paths so that if you create PR-1 for Job 1, C1PRO will store files you had configured for Job 1, etc.
True, you could use absolute paths (regardless where your images are, your output will be always in the same location). I personally like to keep everything in one place and I like to have everything under the main image folder (I use the same strategy for LR and C1).
With C1 (sessions), you need to setup the session before you import/copy your images to the hard drive. I was happy when they introduced catalogs (you could import your old images without creating unwanted folder structures), unfortunately I had to go back to v6 due to constant crashes and slow downs. Even the new catalog system can be improved (too bad that Phase is resistant to it until people start bitchin' loudly about it; when you make a suggestion their response is that people don't need it).