What is the difference between the ARMS SIR #45 and #46

I have an aimpoint M2 on Arms 22m68 mounts and ITT night vision, which SIR system would be better suited for these equipment.

what part of the #46 SIR slimmer?

The #45 is the widest of all SIRS and it is dedicated to one height and/or the PEQ2 mt. It's a STD. CAR length forearm, it has the best cooling capabilities of all SIRS but is wider than the slimlines by approximately .25", and that feels a lot wider than it sounds.

The #46C, 50C and M, #58, #58MOD and the #59 are all slim line in configuration and all will mount both of your sights very well.  The #46 is dedicated to either a 1913 rail or the rail flips to a dedicated PEQ2 mount, in front of the receiver portion of the SIR.

The #50C or M, 58MOD bothe STD. CAR forearm length SIRS are bi-level and will allow you to use an optional rail that will extend the higher of the 2 SIR rails all the way to the front sight tower, or, you can leave the rail off and you have a Bi-level settup that allows both of your sights to mount on the higher rsil, and/or an EOTech type sight on the lower rail, either the Ainpoint on the higher rail, or the EO on the lower will co-witness w/ you Iron sights.

On midlenth gas sysytem type uppers the #58, will work for you, and it too is a bilevel like the above.

On 20" gas sytem setups and/or Dissipator type settups you can use the #59 SIR and it is another Bi-level.

#45 C or M.
#46 C only
#50 C or M
#58MOD M only
#58 M only (midlength gas system)
#59 M only (Std. 20" or Dissipator length gas system)

(M requires the removal of the delta ring assembly, easily and inexpensively done w/ a Dremel, or by removing the gas tube, then barrel, and removing the delta ring asssy.)

Hope it helps.

will the aimpoint on Arms mount 22m68 Co-witness with the iron sights of the SIR #45?

Yes, the std. front sight post, or the PRI FUFS and the Aimpoint M2 or ML2 in an ARMS #22M68, and the #40, 40A, or 40L will all co-witness.