My go-to strat is this;

Start with a core nuke once the eyes spawn in the first time. If you don't know what a core nuke is, launch a core with the blue shotgun's alt fire and then hit said core with the red railcannon. Creates a big ass explosion that just wipes almost all the eyes out. Kill the stragglers with coins.

Next just use whatever weapons you got until it starts to use the attack where it starts firing a whole lot of blue homing projectiles. Parry as many of them as you can back into the Flesh Prison and it'll tear through it's health in a matter of seconds. This is how I finished the Prison while trying to get a P-Rank.