"will I leave it unchecked?"
You start the reconciliation. In the second screen, at the bottom, you click on Matched. You provide the date, for the statement cutoff, so that it does not Checkmark anything that has already been Verified (lightning bolt) but is not on this statement.
You checkmark anything that Is on that statement and has cleared the bank, whether or not you also use Banking Downloads as a helper function.
"
If you have a good resource/online training/book, please let me know."
There are video tutorials here, and two are for Banking:
Desktop PC program video tutorials
And this:
http://fi.intuit.com/support/gsg/dl/QBW17_GSG.pdf
