Add Microsoft XPS Document Writer as a cheque-printer if you want to avoid printing useless hard copies - you don't have to do this - and in cheque-writer select the "Prior to Current Date" option to enter a back-dated ACH. Note that for some reason it'll only let you go back one month at most and that the invoice(s) you want to pay must be marked as ACH in their payment method - you can edit the invoice in A/P to reflect that. This will let you pay mutiple invoices on one ACH if you wish as well as make partial payments.
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).
Maintenance-Financial Designer-Layout-Select the report-Edit then Right-click on the % column-header and click on the % calculation option. Go to the Edit tab and select the expense you want from the left window and the revenue you want from the right window, click Append, never click on Replace. Save. Do the same for your other % columns or copy from this one.
They are location identifiers for a scenario where you have multiple P&Ls feeding into one balance sheet. In that case each set of P&L codes will have the same suffix all the way down - eg 9999.100 for the first P&L, 9999.200 for the second P&L and so on. You'll have a separate P&L for each store but one balance sheet and one trial balance.
I don't think there's any reason to use them for any other purpose. You can if you want - might be helpful for exporting to Excel for instance - but M3 doesn't use them except as shown above. Also, since Financial Designer keys off account names, not account numbers, it can get a bit confusing if you're not careful.
I've never tried day-by-day but I believe you have to do the days as rows under each month, per G/L account, not as columns.