For some reason under the my added employees its linked two employees together as one entry. It also made one of my employees three different usernames.

Welcome to the Community space, Tri.

I want to be sure I can provide the best answer to your concern in managing your employees in QuickBooks Online (QBO). Before starting, I'd just like to gather more details about the issue. 

Can you please share in which area you're having the problem? A screenshot will help us big time to visualize the issue further. What transaction you are tying to do that leads you to the issue.

I appreciate any information you can provide. I'll be on the lookout for your response. Enjoy your day.