The smallest edit would be to modify the ttt_random_ammo entity. It calls ents.TTT.GetSpawnableAmmo(), which is returns a hardcoded table of ammo entity classnames. You could replace that with your own hardcoded list that includes your ammo entity, for example. You could also add your entity name to that table, eg.:
local ammos = ents.TTT.GetSpawnableAmmo()
ammos = table.Copy(ammos) -- don't want to edit this table directly
table.insert(ammos, "my_custom_ammo")
-- leave rest alone
A much better solution would be for me to make random ammo find entities to spawn by looking at ENT.AutoSpawnable like weapons, which is something I'll put on my list.
edit: The latest SVN build of TTT now has this implemented. If you run that version, you can just set ENT.AutoSpawnable = true, and random ammo spawns will use that ammo entity.