I just bought a new iPhone 5 and used it before restoring the backup from my old iPhone 4. Now I would like to restore the backup from my old phone without loosing the text messages already on my new phone. If I back up the new phone first and then restore the backup from the old phone, will the content from the new phone be lost?
When you restore the backup from your old phone all content currently on the phone will be erased. There is no official or user friendly way to merge iOS backup files. The methods that do exist are very hackie and involve jailbreaking your phone first but none of them are currently compatible with iOS 6.
While there is currently no way for you to merge the two SMS files together you don't have to completely loose the messages that are already on your phone. You can use a program such as PhoneView or iExplorer to retrieve the SMS files from your new phone before you restore the backup and store them as a text file. I personaly use PhoneView, but both programs (as well as a slew of others which I'm sure other folks will by happy to point out) work equally well.
As a final note, if merging the the text messages from the two backups is the only way to go for you, there is a method that is not currently compatible with iOS 6 but likely will be at some point in the future. As I said above, it's hackie and may require a jailbreak but once it's updated to work with iOS 6 will do what you're asking for. The script is available at https://smsmerge.homedns.org. I have not used this personally and can't vouch for it's safety, security or effectiveness but it has a pretty long standing history and a decent reputation online.