Don't see how its a disadvantage. But, you are not doing it right regardless. You should not use AFR mode as there is already a default profile that is correct for bf3.
For science.
High:
http://i.imgur.com/Xuca3.jpg
Ultra:
http://i.imgur.com/5INr2.jpg
High:
http://i.imgur.com/Xciy2.jpg
Ultra:
http://i.imgur.com/OXH8R.jpg
There is a pretty large difference in the distance detail with high vs ultra. Now all I need is a 1gb and 2gb card for more...
I just blob a ton of it on the die in an X shape and let it ooze wherever it wants to go.
If you wanted to be anal about it, then the spread method would be the best.
just go res/pump>cpu>mobo>gpu>rad>rad>rad>
Loop order doesn't really matter, and radiators are pretty low restriction. I run two 3x120 rads, 3 gpu waterblocks, and a cpu block. I still have decent flow rate with a single pump.
CPU limit and it sounds like you are using hacked drivers since you are using an 8800gtx for physx... Remove the 8800 paper weight and install proper 11.12 RC11 drivers.
http://support.amd.com/us/kbarticles/Pages/RC11Driver.aspx
Also what res are you playing with?