I captured some video in 1080/24p and 720/60p. The 60p footage will be used for slow-motion only. I will be outputting to 1280/720 for Vimeo.

Should I work in a 1080 timeline and upscale the 720 footage to fit the composition size only to render to 720? Or should I work in a 720 timeline?

Work in a 720 timeline. Upscaling is far worse than down scaling and since your end result is 720 anyway, use that as your sequence settings. Use motion/scale to fit your 1080 footage in.

And you'll have the added opportunity to pan and scan your 1080 clips.