Complex sentence: The US Army used a slightly different naming system from the Navy; instead of their own system of M-numbers, they referred to the LVTs by Mark number using roman numerals rather than Arabic numerals.
Split into simpler sentences: The US Army used a different naming system from the Navy. Instead of using the usual Army system of Model or M-numbers, they referred to the LVTs by Mark number using roman numerals rather than Arabic numerals.