Correct, if you have two sites trying to run as different users but share the same code base or portions in a common directory with SuPHP enaled, it won't work. SuPHP basically ensures folders match the owner. There's a good post about it on cPanel's forums: http://forums.cpanel.net/f5/suphp-symbolic-links-reseller-account-212102.html#post873521
Updated; Since you have root access and control all the sites on the server you can disable SuPHP as mentioned. I've personally found no real benefit of SuPHP if you own and actively manage all the sites. The purpose of SuPHP is basically to restrict what someone can do if they get access to any one of your PHP sites by limiting where they can go by user account.
Keep in mind that by disabling it, if you do have a security breach that it's common for attackers to search every writable directory and inject things like JS malware and PHP backdoor shells to your server. It means the damage could be more widespread.
Using a good web application firewall like mod_security is good and more worthwhile IMO. It can inspect POST/GET requests for SQL injections, etc. You can customize the rules, but it has a learning curve. Basically it bolts onto Apache.