Although it is recommended to have one Apple ID for all Apple services, you can use two different Apple IDs for iCloud and iTunes store purchases.
If you want to use different Apple IDs, then you will need to edit your settings accordingly to get all of the benefits of iCloud. Here is how:
iPad, iPhone and iPod touch:
- Settings > iCloud and enter your iCloud Apple ID
- Settings > Store and sign in the Apple ID for your store purchases
- Navigate Menu > System Preferences > iCloud and enter your iCloud Apple ID
- Locate iTunes > iTunes Store and enter your store purchases Apple ID
- Windows Start menu, choose Control Panel > Network and Internet > iCloud and enter the Apple ID for iCloud (you need iCloud Control Panel for Windows software, read this article for more info).
- Launch iTunes > iTunes Store and sign in your store purchases Apple ID.