Q: I have a different Apple Id for iCloud and for AppStore, what can I do?

Sign into iCloud with the one and the App Store/iTunes with the other: there's no conflict about doing this.

Hello!

Are you 100% sure it's a different Apple ID? Please log in here "manage your Apple ID" - https://id.apple.com/

Once logged in, check to see if your Apple ID isn't comprised of both the email addresses you've been noticing on your iPad.

If you discover that you really are using two Apple ID's and you want to "merge" them, use your iTunes Store email address to create an iCloud account. Creating an iCloud account: Frequently Asked Questions - Apple Support

Then, use this guide to create back-ups of your CURRENT iCloud account and later on import that data into your new account (if you care about your iCloud data at all, that is) Archive or make copies of your iCloud data - Apple Support