I think you are combining EQ and Crossover together when they are two different things. Or maybe using EQ in place of Crossover.
If you want to use the Low Pass crossover on your deck its common to just turn your amp low pass crossover setting to the highers frequency- usually all the way clockwise.
In general:
All of your batteries in the back should be grounded to each other and at LEAST one run grounded to the frame in the back.
All of your batteries in the back should have all positive cables connected to each other and at LEAST one run going to the front of the vehicle (connected to either Bat+ or Alt+)
I think this is what the shop was trying to say.
Feb 15, 2011 - High Point, NC
Where I'm at is not where I'm from and where I'm from is not where I was born.
Born in Bronx, NY
Grew up in Apopka, FL <--this is where I'm from