How to Make Portal 2 Mod?
I've found the dev wiki entry, but I still don't understand. What do put into a vpk file?
Honestly, don't try to make a whole mod only because you want to publish a number of maps altogether on the same (custom) theme or something, just make a mappack instead 
Anyways, you can take a look to this guide. Not so sure if you meant you already read this one, but just in cases.
A VPK file is a special packed file with a lot of content inside that the most recent Valve games load right when you run the game. In Portal2 there is a priority you should know with regards to the "loading order" of the files. VPK files content is loaded over whatever other files there are into the Portal2 directories for example. Also, whatever DLC foler (and its VPK files inside) ended up by a higher number is loaded over DLC folders followed up by lower number (portal2_dlc2 folder will have priority over the portal2_dlc1 folder).
In order to build a mod, you must have at least 1 VPK file under your mod's folder and called pak01_dir.VPK (altogether with a number of other mandatory files ). Usually, you put into it as many custom files as you want your mod to use 
useful tools and stuff here on TWP 
[spoiler]
[/spoiler]
Anyways, you can take a look to this guide. Not so sure if you meant you already read this one, but just in cases.
A VPK file is a special packed file with a lot of content inside that the most recent Valve games load right when you run the game. In Portal2 there is a priority you should know with regards to the "loading order" of the files. VPK files content is loaded over whatever other files there are into the Portal2 directories for example. Also, whatever DLC foler (and its VPK files inside) ended up by a higher number is loaded over DLC folders followed up by lower number (portal2_dlc2 folder will have priority over the portal2_dlc1 folder).
In order to build a mod, you must have at least 1 VPK file under your mod's folder and called pak01_dir.VPK (altogether with a number of other mandatory files ). Usually, you put into it as many custom files as you want your mod to use
A Mappack is what I had in mind 