To set up an online server for minecraft, you will need to download a Jar called Minecraft Forge, you also need a program such as "Log me in Hamachi" to set up a VPN in order to have an IP for the server and your friends to connect to, to my knowledge the current version of Minecraft doesn't support Forge so you may be at a bit of a disadvantage there in means of the mods, if that is the case you will need to run the server and Minecraft in an earlier version that supports Forge,
Now for the installation.
Step 1:Download the Minecraft Forge installer fromhttp://www.minecraftforge.net/forum/index.php?action=files
Step 2:Open the installer and select "Install Server". Then select the server Directory. And finally press Okay.
Step 3:Go into your server Directory and open "minecraft_server."the version of server you have installed". It will open a new window and load the server.
Step 4:Now in the command line type "/stop". It will close. After that in your minecraft server Directoy create a folder named "mods".
Step 5:Put all of your mods zip files in the "mods" folder.
Step 6:Launch the server and see if everything worked.
There's usually some trial and error with the mods, some will and won't work with some version etc.