Do larger RAM sticks run any hotter than smaller sticks? If so, is it all more or less inconsequential with the airflow Mac Pro cases provide?
Technically, Yes, larger sticks tend to consume more energy than smaller capacity sticks (more parts on the PCB = more power consumed = more power converted to heat). But this is on the specific case that there are in fact more memory chips on the DIMM.
When you consider higher density memory chips however, this may not hold true (i.e. double the memory density, so you could get an 8GB stick with the same number of memory chips as a 4GB stick constructed of memory chips that are half the density of those used in the 8GB stick).
Fortunately, DDR3 doesn't run as hot as Fully Buffered DDR2 used in 2006 - 2008 (hint: standard DDR3 sticks, including ECC variants, don't require a heat sink on it). Another thing to consider, is the DIMM slots do get decent airflow in the current MP's as well, so there's no need to worry about this.
if i was to put 2 of these in a 12 core 2010 MP how would I need to install them? 1 in the upper memory compartment and 1 in the lower? assuming no other RAMs are used.
What system are you trying to put them in?
I ask, as the 2009 and 2010's are the only systems that can use DDR3 RDIMM's (impression you do need DDR3, but need to be sure you're not running a 2006 - 2008), and the DIMM slots are located on the CPU tray (daughterboard), rather than the memory risers in previous Intel based MP's (2006 - 2008).
If you are using a 2009/10, then stuff one in DIMM slot 1 and DIMM slot 2 (take a look
here; Memory How-To .pdf from Apple).
Please note, that you'll need to remove the OEM memory or any other that's not RDIMM (OEM = Unbuffered, aka UDIMM, as are the 4GB and smaller sticks from OWC).
also how would a 12core perform with 1066mhz rams instead of 1333?
This will depend on the software you're using.
But for most users, it won't matter, as there's not a lot of software that can actually utilize the memory bandwidth of the memory controllers in your system. Capacity will mean more for the user than the frequency it runs at.