Guys I have a problem. So I have a track done and getting my mix to sound as good as I can get it to be. and I'm using reference tracks to know how my track really should sound.

So when gain staging at first I do it so that the loudest part of my song is at -6db more or less. So I get a reference track and place it so that its volume is also at -6 db so I can compare it at the same volumes.

The thing is when I start making adjustments to my track so it matches my reference track I always find myself in a position that when it sounds the same as my reference track the overall volume of my mix is at -6 db, but I have some peaks that reach almost -3 db!

Obviously the reference track is mastered and has a limiter and nothing crosses -6 dbs, but I can't get my mix to sound the same without getting those peaks out of the way. I tried placing a limiter, but it just kills the mix.... I don't know what to do

Just set them both to about the same volume, if you're only checking the mix. Ignore the meter, use your ears to set the volume, and worry about the master when you get there.

if you mix one instrument at a time , you should probably know what causing the peak .
even a small hi hat can can cause a peak if it hits the same time as the kick or snare (or any other instrument with an transiet)
watch your master and find where you get your peak, and mute every instrument thats playing at the time .
i had the sime problem last night,a tom was hitting the same time as the sub so i just faded the sub just a little and then it was ok .