Yes you can use different Apple IDs for iCloud and store purchases. This is totally Apple approved and so you don't have to worry. You cannot merge two apple accounts into one. You can however use multiple Apple IDs 1 for iCloud and 1 for store purchases which would include iTunes in the Cloud and iTunes Match. The next question that would arise would be - now that I have purchased music, apps and books using multiple IDs how to get all of it onto my iOS device. To do that you would need to firstly First copy all of your purchased content so it is on the same Mac or PC with iTunes. This computer should be the one you sync your device with.
If you are wondering how to get all this done, apple has advanced support for it's users and you can avail detailed instructions from the Apple Support site. Using multiple IDs comes with its advantages. Now all members of the family can access the same account using multiple IDs and purchasing and using all of this is totally legal.
Source: Apple Support