This might help a little bit, though it's not the whole story:
Until you're more comfortable with how it works you should try not to have anything hit your G/L cash accounts except for Cash Management entries.
A JEMN or JERC/JERV will not show up in Cash Management unless you make a corresponding entry in CM to match it (but without a G/L code). This is not actually a one-sided entry, it's just a memo item to bring CM into line with the G/L, but generally they're best avoided.
Daily Report setup is key, make sure you have your settlements identified as Cash or Credit Card and make sure the Daily Report line item description exactly matches the Enterprise Advanced Cash Management types (you can add to or edit these as much as you want).