This is one annoying battle.
Have gauss (3 shots to take down flying enemies) and minigun (for the same enemies).
Hide behind the ships bridge and sty there no matter what you are yelled at to do. When Hellena commands you to shoot it with the TEC - look from the left side and then the right side (for the second arm). Watch out for fires - they can drain your health very unexpectedly. Also wait for the boss to fire its main caliber and then start aiming with the TEC (it's main cannon is very random at killing you, so better safe then sorry).
When the belly is ready for blasting super sprint from the LEFT side (the right side is on fire) and minigun. After belly opens you get a checkpoint and will you probably die. Restart and super sprint back to your hiding place. Wait for 3 flying enemies and 3 smaller jumping one, kill them, sprint back to main deck and hide behind the burning helicopter on the left - from there you can easily aim and fire at the blasted belly.
Hope this helps.