2nd Stage is using all of my fuel and oxidizer from my 3rd stage

[Oreilus]

First time asking a question on here so apologies if it's in the wrong location.  I played KSP a bunch a few months ago and never had this problem, now I can't find a way to stop the 2nd stage from using all of the fuel in the fuel cells above the third stage.

[Superfluous J]

By "Fuel Cells" I assume you mean "Fuel Tanks"

What is between your stages? docking ports (which you can turn staging on for) allow crossfeeding by default. Decouplers now have the option to turn on crossfeed, and if so they'll happily suck your upper tanks dry. In either case, you'll have to turn it off.

If that's not it then I don't know. I'll need to see your ship and a list of mods you're using, if any.

[Vanamonde]

We would need to see a pic of the ship. 

Also, moved to Gameplay Questions, since it's not a tutorial.