It requires a bit of luck since the projectiles come out too fast to avoid (at least talking about this red amoeba lieutenant I killed recently) so the hits you take mostly depend on how many bullets the amoeba decides to spit out in each attack. I've noticed that right below the amoeba is your best bet as shot numbers divisible by 4 seem fairly rare. Then just hold down the mouse buttons for the white cutter and whatever other ranged spell you use (in my new world I'm using ball lightning and the cutter, probably the highest DPS option). Ghosts go down to that spell combo fairly easily but you need to down them before you're cornered by them and their miasma.
Even the red amoeba's attacks are completely dodgeable.
The trick is figuring out HOW.
Hint, watch the angles. Even when it sprays it's maximum amount of bullets at once, there are points underneath it where you can stand to avoid it's attacks. BUT, you have to keep in mind it's movement, which can change just WHERE those safe points are.
Also, watch the distance. The further you are from the thing, the better; this is where good knowledge of the surrounding area is key. Learn where the maximum effective range of your attack is (preferrably something like Energy Pulse), and try to stay at that range. And if the thing starts to move towards the floor, move even further away from it, even if that means going out of range. Dont attack it if it isnt high above you.
Those are the tips I can think of for dealing with these. I went through a tower last night that had nothing but the red amoebas, and in all honesty, I didn't actually get hit all that often.