To determine if your setup is complete, run a Balance Sheet report from Fund Accounting - i.e. Fund Accounting / Reports / Balance Sheet.
You should see the beginning balances that you entered in the setup wizard. If something is not correct, hit the RESET ACCOUNTING button and start the wizard again.
1) You can identify the chequing accounts as you mentioned. I would give them account numbers like:
2) When you receive $1,000 in your "line-of-credit" chequing account, enter it like this:
DB 01-1170-000 line-of-credit chequing $1,000
CR 01-2170-000 chequing liability $1,000