just a few questions about wiring

OK, so what are you guys doing with the things you don't need or want, just cut the wire at the connector?
What about things like the Evaporative Emission Solenoid Control, Fuel Pump Module, Leak Detection Pump, Auto Shutdown Relay, and Battery temp Sensor?
Do I have to run my charging system through this PCM or can it stay a part of the original wiring?
You guys are the best. Any help would be appreciated.
Tom