I am trying to host a modded server for me and my friends and I have installed the client and server versions of forge to the locations I needed. I started the server the first time to install the elua then a second time to add the various files and folders I need to but every time I have tried it does not add a mods folder. I can run the server normally as a vanilla server but I can't get it to accept mods am I missing something or do I have to create my own mods folder.

It sounds like you are starting a vanilla server.

How are you starting the server?

I have two options one is minecraft_server.1.12.2.jar the other is forge-1.12.2-14.23.5.2830-universal.jar and the first .jar works but I can't get the universal.jar to do anything, I read somewhere to run it in the command line but I don't know how to do that either. I'm pretty new to this.

Running the first one would start a vanilla server.

Try running the second one from command line via

java -jar <file_name>

. Remember to cd into the directory first.

It worked thank you. Will I have to do this every time or just this one time?

You will have to do this every time you want to launch the server.