Even if you use the same iCloud account for both iPads it will know they are different and create different backups. It is essential to have given them different names under Settings > General > About > Name; so that you can tell which backup is for which iPad.
However, since Apple only gives you 5GB of free iCloud space, you may want to follow Johanna's advice and have a separate iCloud account for each iPad. I back up both my iPhone and iPad under the same iCloud account, and while I've never exceeded the 5GB limit, I have come close. Not an issue for me, since I actually have more than 5GB of iCloud data (a combination of legacy and cheap upgraded deals I lucked into), but it might be a problem for you if you keep a lot of apps and data on the iPads.
Just to be clear, it is possible to have different iTunes and iCloud accounts on the same iPad; so you can keep sharing apps and music but differentiate your storage space, email, calendars, contacts, and other iCloud services.