Hi Josh,
Your question...
"Judd - Is the diagram you posted with the leads going from the +5 and the - 10 going to the charge controller correct?"
Yes, the point at which you connect to the battery bank becomes critical because of the voltage drops in the individual interconnects. The +5 and -10 connection gives the best balance. The two most commonly used ways is (+1, -14 as advised by some manufacturers) and (+1 and -2 NOT a good idea). In the system I had drawn there was a Voltage differential of 2.8v across bats 13,14 when charge controller/inverter were connected to bats 1,2. This caused 2 batteries to fail prematurely as they never got fully charged and the system was not properly sized Panels/Storage/Wiring. This should not be a problem for you as the Panels, inverter, MPPT,& Wire Size you have selected are well matched. My stating the importance of this for you is the selection of AGM, which is much less maintenance but does not allow for easy "equalizing" as batteries age, get abused, etc. So where you connect is more important
Your Question:
"Also which leads would go to the inverter?"
As I have drawn above.... Red POS (+5) & Black NEG (-10) connect to both MPPT and inverter (parallel) I checked the manual for Samlex Inverter http://www.samlexamerica.com/customer_support/pdf/Manuals/ST_Series_Manual_Aug2009.pdf
With #2 wire the Positive line should have have a 100A fuse in series and no disconnect is needed for inverter as the Samlex already has one built in. Max distance from Battery Connection point to Inverter with #2 wire is 3-6 feet.
I tried to envision the physical placement of your batteries with 21" wire lengths. You must have a different layout. If as above the width is 26" W, 91"L, & 9" High (BCI Group 31). Can't do with 21" lengths as a "home run" for each 24v battery pair?? Can you give a better description of Physical placement?
Also, the MPPT manual:
http://www.blueskyenergyinc.com/uploads/pdf/Manual_BSE_SB50L.pdf
Shows two rather skimpy connection points to Batteries. Do you have some type of Terminal block / Bus for +24v? It is internally fused ..... but an external fuse might be a lot easier to get to... just a thought.
Judd