1) Receive document.
2) Scan with Fujitsu Scansnap S1500 in about 10 seconds. $380 on sale, but so far worth it over cheap all-in-one scanners it's not even funny. Seriously, don't even bother going paperless unless you get a real document scanner.
3) Save PDF to simple software RAID-1 mirror of two 2TB drives. (Takes about 5 seconds to setup from disk management in Windows.) This should protect against sudden drive failure taking everything.
4) Backup nightly to external drive swapped off-site every other month. This should protect from accidental deletions, fires, etc. Bonus points if backup drive is ioSafe fire proof variety.
5) Throw away original. Only exception is official documents like titles, marriage certificate, etc.. Yes, I even throw away W2s and the like. My taxes are 100 percent digital nowadays.
6) Check and test restore from those backups on a semi-regular basis, and you're done!