I have a 120 Watt Crate GT65/212 Guitar Amp. It's pretty nice but when i am on the clean setting the low is increadibly to bassy. The other five strings are normal then the 6th is overpowered.

I tried turning it all the way down messing with mid, low high nobs on amp. Still the low E continued to overpower.

It still does it when i adjust it through my effects pedal as well.

Is the amp just naturally low E? Or can i fix this someway?

If i can't fix it, what are some good sounded amps used for Rock and Metal?
Its probably all in the fact you have an Invader, Im assuming at the bridge of your guitar. Thats an insanely powerful pickup. Try lowering the top side (the side that sits under your E, A, and D strings) down into the body a bit and raising the bottom side of it (the side that sits under your G, B, and e strings).
hmm really. I didn't think it could be that.
How would i go about doing that?
I have never messed with Pickups personally.
Theres screws on both sides of the pickups. Tighten them to raise the pickup closer to the strings and loosen them to drop it down into the body of the guitar.

The closer the pickup to the strings, the more output it has. Which is good for distortion, but not for cleans. It makes it sound too powerful and muddy.

The further away the less output. Which is good for cleans because it adds clarity, but it makes the distortion sound weaker.