First, follow the instructions in here:

http://wiki.teamfortress.com/wiki/Dedicated_server_configuration

Then, what you need to know for MvM and QuickPlay:

You need to add

tf_mm_servermode 2

and

tf_mm_strict 1

(the later is not required, but it will make your server run only in matchmaking mode, but it will NOT allow manual connects) to your config (server.cfg).

You also need a “TF Gameserver account”, which you can get easily by following these steps:

• Log on to your (personal) Steam account on your computer. Start up TF2.
• Open up the console (usually with the ` key)
• Type:

  cl_gameserver_create_identity

Your game console will then output something similar to this:

] cl_gameserver_create_identity
Request to create a game server account sent--please wait.
Game server account created successfully!

Set these convars on your game server to have it log in and receive benefits:

tf_server_identity_account_id XXXXX
tf_server_identity_token "XXXXXXXXXXXXXXX"

Take the last 2 lines

tf_server_identity_account_id XXXXX
tf_server_identity_token "XXXXXXXXXXXXXXX"

and paste them into your server config (server.cfg).

Next up, you need to set-up your mapcycle.txt to only contain MvM maps. As of writing this, they are:

mvm_decoy
mvm_mannworks
mvm_coaltown

Now, simply run your server while booting it directly into a MvM map with a limit of 32 players (this IS required!).

./srcds_run -game tf +map mvm_coaltown.bsp -maxplayers 32