If you want to sync contacts and other data with a shared account your iCloud data and photo stream photos will be merged. If you want to keep them separated, move one of the phones to a separate iCloud account with a separate ID. You can still share the same ID for iTunes purchases; it does not need to be the same as the ID you use for iCloud.
To migrate one of the phones to another account, decide which phone will be keeping the current iCloud account. On the one that will be changing accounts, if there are any photo stream photos that you want to keep on the phone, save these to the camera roll by opening the my photo stream album, tapping Edit, tap the photos , tap Share and tap Save to Camera Roll. Also, if there are any notes that you are syncing with iCloud that you want to copy to the new account, open them one at a time and email them to yourself so they can be recreated after changing accounts.
Once this is done, go to Settings>iCloud, scroll to the bottom and tap Delete Account. (This will only delete the account from this phone, not from iCloud. The phone that will be keeping the account will not be effected by this.) When prompted about what to do with the iCloud data, choose Keep On My iPhone. Next, set up a new iCloud account using a different Apple ID (if you don't have one, tap Get a Free Apple ID at the bottom). Then turn iCloud data syncing for contacts, etc. back to On, and when prompted about merging with iCloud, choose Merge. This will upload the data to the new account.
Finally, if you have any data that you don't want in either account, you will then have to go to icloud.com on your computer and sign into each iCloud account separately and manually delete the data you don't want from each account.
To prevent apps purchased on one phone from automatically downloading to the other, go to Settings>iTunes & App Stores and turn Apps to Off under Automatic Downloads.