Well I'm not really sure what you are doing currently, I assume just scanning them in as image files.
I've not used the most recent Sage or QuickBooks in any depth yet but did pick up on some hints previously about tying in document scanning. There's no hints about it on the Sage website (though I'm hardly surprised), Quickbooks website does list as a feature "Just scan in and attach related documents to particular accounts or projects, so you have everything you need in one place for easy reference at tax time."
Alternatively, simply use reference numbers that refer to the scanned image filename or tag. Most of that can probably be automated (both file name and reference incrementing by 1) but you should check every n'th entry per batch. If you simply need a "smart" list of bills to pay, you could just tie it into a spreadsheet/database.