So really you are just using at like a till rather than accounting for every transaction as you go. So maybe this guide will be of more use?
http://community.quickfile.co.uk/t/accounting-for-daily-takings/8911
Although you are somewhere between the two so it will probably still need some manual tweaking. The general thing is to make sure you have records available, I do pretty much everything through Quickfile so I have a single point of reference for auditing if required. However, you could just add a single entry as you do now as long as you keep copies of the reports and sales to fill in the blanks if required.
As for transfers between accounts, what do you do now with the money in PayPal? If it is transferred to the current account then when it is tagged from there then it will show in the PayPal account also. If you don’t take any money out of the PayPal account then you don’t need to show any transfers.