Lost Half my Amps to the battery

Welcome to the forum Matt.

If you have an accurate voltmeter, measure the voltage at the battery terminals and see what you have. Depending on how the charge controller is programmed and what type of battery you have, the charging voltage will probably be in the 14.4 to 14.8 volt range.

If the battery is at the "absorb" voltage setting, the battery is controlling the charging current (80% state of charge, near maximum current possible from your solar array, as battery approaches 90%+ state of charge, the absorb current will drop--EVentually to 2% or less of your battery's AH capacity--I.e., 100 AH will drop below 2 amps--and even lower if left on charge).

If your battery voltage is 13.x volts or lower, then the charge controller should be outputting the maximum charging current available from the solar array. This is "bulk mode" where the charging current is limited by the solar array+sun and (depending on charge controller) by the charge controller itself (you have a "large" charge controller, so I do not expect it is limiting charging current in bulk).

If you determine that the charging current is too low (battery not fully charged and/or you have good sized DC load current), then wiring can be an issue.

Make sure the wiring from the charge controller is short and heavy (low resistance, bolted connections and NOT using alligator clamps. Your wiring from the charge controller to the battery bank should be no more than ~0.05 to 0.10 volt drop (for a 12 volt battery bank).

You are doing it correctly by adding wire length between the solar panels and the charge controller--But you need to ensure that these cables are heavy enough gauge that you don't lose more than a volt or two from array to the charge controller. You can use a voltage drop calculator to figure this out.

http://www.calculator.net/voltage-drop-calculator.html

-Bill