Normally the battery is connected to the alternator through the ammeter gauge in your dash. The power loads from your car sits on the alternator side of the ammeter gauge. When the alternator is charging your battery, the gauge is therefore able to show this. Likewise, if the power loads are consuming more power than the alternator can provide, the battery will supplement, and then the gauge will show that the battery is discharging.
You said you disconnected the ammeter gauge and hooked the two wires together. BUT, you ALSO added a new cable from the alternator to the battery. So if I am understanding your mods correctly, you now have two somewhat parallel paths that electricity can take, one is your heavy 4 gauge wire, but the other is through your stock wiring. It is still there...