Solved I really need help. I am complete nub.

What I need help with is... That I don't know what to connect what to what with 2 EXE's. Do I just connect the connect server to the proxy then add a new Username/pass in the connect file to connect to the minecraft server? Please help me. I'm really confuzed.

For indepth help need to know what your platform is for starters. Are you running on linux or windows?
for a general setup you first need to setup your proxy servers using connect and proxy. you then need to download the connect plugin for your servers and set them up in your go proxy you will have a user name and password that will match the config file in your minecraft plugins folder.
the plugins for your minecraft servers are bukkit-connect bukkit-portal and bukkit-bukkitportalcommand they go into your plugins folder

@Curtis3321 I am running windows 8, And I already have all the needed software.

Read and watch the tutorial @Minecrafteds , it should answer all your questions: http://www.lilypadmc.org/threads/setting-up-a-golilypad-server-ssh-centos.380/

@The_Zip Yeah.... I seriously can't run CentOS... =/ Just doesnt work...

You don't need to run CentOS, the tutorial is just using CentOS.

Have you ever set up a regular bukkit/spigot/or vanilla minecraft server? If so do everything the exact same way, but use the windows-amd64(The command to start would be './connect-windows-amd64.exe '. Other than that, follow the tutorial on how to configure everything.

@The_Zip I just did everything it said, And it didn't work... , And yes, I have had run a Factions / Prison / Creative BungeeCord server, I just want to try using LilyPad this time around

@The_Zip Wow, How could I be so foolish? Its complicated to explain...

Ummm? So did you get it working?

@The_Zip Yes I did, But one problem. I can't add more than one server...

Post your configs please.