Well, if you're playing this mission on NORMAL, then just use the least costly Grenade launchers on your back. It's what I did.
Also, tune your mech to be extremely fast, do not worry about defense/AP. Basically, just make it to where you can overboost a lot, and are very fast. (Turn your KP output all the way up, and then your overboost)
Other than that, memorize where each Sub spawns, and which ones spawn first.
(Hopefully, I have the right mission in mind, I traded this game ages ago once I got all 1000)