Hey,
I was there last september and stayed in a hotel near the vatican and all the bus routes. Can't remeber the name but i'll try and dig it out.
I used
venere.com to get my accomadation for everywhere i stayed in italy. Found it very good because it shows all the different areas of the city you can stay and search accordingly. you can also search by hotel type.
Buy a Lonely Planet book as well because they give you all the touristy details: hotels, resturants, bars, sites etc. I'd highly recommend them. Prob get them in any Easons or big book store.
Hope this helps.
Oh, bring comfy shoes because you'll probably end up doing a lot of walking between sites!!
Colin