They way you have it wired now, if you see the ammeter showing discharge when driving with the lights, wiper, or heater fan on,
a) then its likely there's resistance in the factiry line from the alternator to the main splice.
b) If that's more than halfway toward 40 amps, fix that sooner than later. Continuously running more 25 or more amps through the 16 gage fusible link may cause it and its connections to get hot...