SSL certificate confusion

I have installed ssl certificates on WebServers using IIS since 6.0 and I need to install one on a server now before going live and although users type a URL into a browser to access the webpage and sign in to perform several types of financial transactions,  The first thing I looked for was the inet pub folder and there was none.  Needless to say there was no IIS of any version and no CSR to submit and no self installation application to install the cert for me.
Now I'm not sure whether or not the ssl certs I use for our web servers are used for this type of application server and I have no clue as how to go about installing an SSL cert without IIS.  Testing is starting and so far I find that  I can't connect with the reason returned being there is no Cert installed in the Root CA Authority store. Can anyone shed some light on this subject for me or at least point me in the right direction so I can get this server secure before going live with it.      Any tips on what the dfferences are between this type of app server and a web server and how to install them on servers without IIS.  Thanks.
Joe DonahueDirector, Technology ServicesAsked:
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David FavorConnect With a Mentor Linux/LXD/WordPress/Hosting SavantCommented: provides free certs + a simple to use client to generate + auto renew certs, before they expire.

This means setup + forget SSL certs that work forever, once you have a correct CRON job (or equivalent) running.

Anytime you require setting up a new cert for another machine, you just duplicate these same steps for any site on any machine.

SSL certs are... SSL certs, so each Webserver will provide docs for how to setup certs + Apache is the gold standard, so if running Apache is an option, use Apache.
David Johnson, CD, MVPConnect With a Mentor OwnerCommented:
what is the OS on the server and are you using apache server? Since you are not using IIS
David FavorLinux/LXD/WordPress/Hosting SavantCommented:
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