I've been through this process and there are a few gotchas (which you'll find if you google similar problems).
Details here: http://youhaventreadthis.tumblr.com/post/394709023/apple-airport-extreme-disk-needs-repair
But in summary:
You can only format the drives by attaching them direct to a Mac (or PC if you must). It's not possible to format a drive connected to the Airport Extreme.
So, connect each drive to the Mac and format it to HFS+ (Mac OS X Extended Journaled). Be sure to set the partition scheme to GUID, as well as format the partition to HFS+.
They are set separately and it's possible to have a drive partitioned as Master Boot Record (likely the factory default) and the partition formatted to HFS+ (or FAT32, the likely factory default format). In this instance the Mac will read them and they'll seem fine when connected via USB but the AE will fail to recognise it, turn the indicator light orange and report "Disk needs repair". This is true even if there is only one partition on the drive.
(The Airport Extreme does not support NTFS but you're using Macs so that shouldn't be an issue).
From there plug them into your USB splitter and plug the splitter into the Airport Extreme. They should now be visible through finder.
To backup through Time Machine you simply open Time Machine preferences (through System Preferences or the Time Machine icon in the bar at the top), specify the drive and you're good.
The first back up will take a long time so it's best to connect your machine directly to the Airport Express using a network cable. Even with this backing up 100Gb could take 10 hours.
One common error is doing the first back up by connecting the hard drive direct to the Mac via USB. This doesn't work - Time Machine won't then recognise that back up file when it's connected via the Airport Express - you need to connect the drive to the Airport Express via USB / Firewire and then connect the Mac to the Airport Extreme using a network cable.
But generally it works fine, I've been doing it for over a year now without problems.