I am not sure about this. If I use octocore FX 8350 1 h sure is better than single core 8h.
Configuring the number of cores, hash size, endgame tablebases support and...pondering on/off and setting the proper use of opening books (if you do match tests between engines) is enough for a start.
For infinite analysis you have to configure maximum hash (irrespective of the engine you use). It means that if your PC has 2048 MB RAM, then your maximum hash size is 1024 MB. For matches between engines it depends on what time control they play. If it's the classical 5' blitz control - 128MB for each engine is enough (reading a big-sized hash file while playing blitz is counter-productive). 256MB hash for each engine is good for matches on 60'+15" time control for example...and so on..
"Large pages" can improve the speed of analysis with 10 to 15 per cents, but not for long (and not every engine can handle them right, too). And besides, you have to be experienced in order to set properly the "large pages" parameters on your PC (if it supports them, of course).
Usually, engines are not good with openings or opening-related positions. That's why their developpers recommend using human-made small opening books (up to 8-15 moves only). Do not rely on proper evaluation of the openings by engines up to the 15th move!
If you let them play in matches on their own, they'll probably start with 1.d4 d5 2. Bf4 Nf6 3.Nc3 Nc6, or similar, all the time.
...And yes, analysing on one core for two hours is better than analysing on two cores for one hour only.