Hi Craig - can I jump in
I have had similar issues with my own clients and, firstly, on the number of "Paid" transactions made available, you are right, this is currently limited, I think, to three and so, with lots of transactions a month from the same customer/supplier, you'd have to import & "Reconcile" on a more regular basis, with latest first I think.
Apologies if I'm telling you something that you already know but the import/explain process is most useful for entries that you have not already entered in the books and some users run their books entirely in this way.
For you and me however, where we will pay off invoices or bills manually, or enter transactions as they happen, all the import/explain process is doing is confirming something you already know but enabling you to double check the amount you entered originally. As Berhan says, this "Reconciliation" element should be available to you by showing "Reconcile" next to a Paid item but if, for whatever reason, you can't see this, then there's no need to delete your original entry & re-input from the statement.
Instead, as long as you are happy that the amount on the statement matches the sum you entered, go to the bank screen itself, find the entry you made, check the check box next to it and hit "Reconcile" at the bottom of the page, this will put a nice green tick next to the item showing that you have reconciled it to the bank statement. You then return to the statement imported and delete the line as it's now redundant.
Some users, who enter most entries manually, do this in a bulk process, ie they look at the statement first, check all the items already entered and "Reconcile" then delete the lines from the CSV, importing only the fresh entries they want to import from the statement.
Hope that's not too confusing or old news.