Keeping users' messages separate

Regular SMS text messages will remain separate on devices since they are handled by the cellular service. iMessages however can be on multiple devices depending on the Apple ID used and other iMessage settings in the Settings section. If you are sharing an Apple ID for iMessage, then messages will appear on all devices using that Apple ID. That is in the iCloud section. You can still use the same Apple ID for music and app purchases, but use a different one for iCloud which would include iMessage.

In my house, we have 3 phones that share the same iCloud ID to enable me to keep track of all 3 devices in Find My iPhone. We do not, however, see each others messages because in the settings area of iMessage, the only thing checked for Send and Receive is the phone number, which keeps the messages segregated to the individual device. This is difficult, however, if you are purposly trying to share with an iPad, which requires the Apple ID. I believe you could still use the Apple ID for that and a single device and still not see messages on the other cellular devices.

The settings in iMessage have nothing to do with backups. However, messages is part of the backup, both in iCloud and if you were to backup in iTunes.

As far as the Send & Receive is concerned, if you only have the phone number checked then only messages sent to the phone number will appear and will only appear on the phone. You need to check the settings on the other devices to make sure they are set for the phone number only as well. The alternative would be to create a iCloud account for each device. As I said earlier, I do it the way I do to simplify the ability to track all 3 devices together. Let me know if you have any further questions regarding this setup.