Upgrading from OBM 2.5 to OBM 3 is easy, but you should take care of the following know issues.
OBM 3 won't work with oPush < oPush 3.0
Before upgrading to OBM 3, you must upgrade oPush. This is mandatory.
Beware that for oPush 3 there's some new system requirements that your infrastructure should meet. All information can found here.
If you have Roundcube installed in the OBM Apache vHost
If you run the webmail under another alias than /webmail you're good, you don't have to do anything.
Otherwise you have to move the running Roundcube instance to another alias because OBM3 embeds its own Roundcube instance that is running on /webmail. That's why you need to rename (or disable) the alias so that URLs in the form of /webmail/... aren't "eaten" by the alias.
If you have some php remi packages installed on CentOS
At a moment, on CentOS, we needed to use non standard packages with a remi prefix. If your installation use them, you first need to remove these packages that are no more needed and you need to install normal php packages. Then check with "rpm -qa|grep php" that you don't have remi packages before upgrading.