Yes set everyhting up in System Config screen first but then you tune the drives thru software using the current loop tuning screen.
In here you can play with the settings or just use Auto which is same as flicking dip switch 4.
99% of time auto works fine so I'd just use that.

In the System Config screen don't worry about the sliders etc they are for tuning resonance and unless you have any problems the default settings will work fine.
The main settings your interested in are at the top. Peak Cur(A) and micro steps. The others you can leave at defaults.
One other setting you may need to change when your setting up the Fault signal to activate the E-stop is the Alarm Signal Low - High option. This will depend on how you do it but often you have to toggle this so it activates when state goes High.