I have those upgrades, but they didn't help me beat either boss. I can't get them down to half health so it isn't like I'm even close to beating them. The secret areas may be obvious to you but I'm clearly missing something. And as progression relies on finding those hidden things I guess that's game over for me.
ah man sorry i realize i sound like a dick. i dont mean to.
so most secret paths are hinted at by details along the entrance to the area. like say, a bush/crystal that you can kind of see sticking out. in dungeons its stuff like broken tiles, or out of place looking details along the walls. they are pretty subtle sometimes but for the most part its easy to see. if i were able to id post some screenshots for you.
a simple tip for boss fighting is NEVER stand still, and always dash. the frog boss can be stunned by the exploding guys he sends out if you can get them to blow up near him. the skeleton boss, you can trick him into destroying his buddies while they are in the crystals. reflect his bullets and shoot back at him. melee is kinda tricky because he has such a small window to counter attack. hes by FAR the hardest boss in the game. even the end boss is easier.