Multiple Domains, One Linode, Broken Permalinks

Hello all! I am attempting to setup two domains on one server, which is working fine for the first domain I set up, however the second domain is having issues with permalinks. I cannot get them setup properly and every thing I have tried in regards to adding Allow Override and Rewrite _____ to the .conf files all wind up redirecting the second domain to the first domain. Is there something wrong with the way I have the .conf files set up? Not sure how to proceed. The article below would have been perfect, if it wasnt deprecated

https://www.digitalocean.com/community/tutorials/how-to-set-up-multiple-wordpress-sites-on-a-single-ubuntu-vps