If Heavy Arms does run on electricity, an EMP from either suit of armor would take it out of commission. End of battle.
If it doesn't for some reason, and if it did fire all 100 or so of it's missiles at once, the combined targeting computers of Iron Man and War Machine can take out 120 at once with their gattling guns that can fire 1000 rounds/sec. So, there stands Heavy Arms, out of missiles trying to manually target and hit the fast and highly maneuverable Iron Man and War Machine with its machine cannon, double gattling gun, catling gun...whatever. Meanwhile, Heavy Arms is being blasted away with War Machines Sub-Nuke missiles, anti-ship missiles, armor piercing shells being fired at 1000 per sec., Iron Man is hurling pulse bolts at him, launching adamantium-tipped scanalyzer missiles through the armor (finding weak points), and for humor covers it in a ploybond adhesive compound so Heavy Arms is getting the crap kicked out of him while stuck in that.....and then to finish him off Stark would send Magnetic Compact Modules at Heavy Arms repelling his atoms from eachother. End of battle.