Step 1
Create a shortcut on the desktop to the MOHAA.exe and then add the following to the Target field in the properties (right-hand mouse click on the shortcut) window.

It will look something like this: Target: X:\Games\MOHAA\MOHAA.exe

Add the following after MOHAA.exe and make sure these is a space between them:
+set dedicated 1 +exec server.cfg

+set dedicated 1
// make it a dedicated server (1=ON 0=OFF)

+exec server.cfg
// Name of the server script you wish to execute. NOTE: Be sure it is in your X:\MOHAA\main\ directory or it will not work

You now should have a shortcut named MOHAA on your desktop with properties that look like this:

Target: X:\Games\MOHAA\MOHAA.exe +set dedicated 1 +exec server.cfg

Click apply! Now onto step 2!

Step 2
Create a server.cfg (create a text file with notepad/editpad whatever, and change the file extent ion to .cfg) script and put it into the MOHAA\main\ directory. The contents of the server.cfg file should be most of the following:

// LANage (example) MoHAA Server Config File

seta sv_hostname LANage_MOHAA_Server
//Set your server name

sets Admin hachiroku
// Display your admin name

sets URL www.lanage.ca
// Display your website URL. Not needed for LAN.

sets Connection T1
// Advertises what speed your Internet server is. Not needed for LAN.

seta sv_gamespy 1
// Advertises your server on Gamespy (1=ON 0=OFF)

// NETWORK SETTINGS

net_noipx 1
// disables the IPX protocol

net_port 12203
// specifies port 12203 for client connections

// SERVER SECURITY

set rconpassword your_password_here
//Set password for the remote console

seta sv_floodProtect 1
//Don't allow players to flood server

seta flood_waitdelay 10

seta flood_persecond 4

seta flood_msgs 4

set sv_pure 1
//Will not allow clients with non-standard pak files to connect.

//SERVER VARIABLES

seta sv_allowDownload 0
// Allow players to download the maps if they don't have them.
// Handy if you are server modded maps (1=ON 0=OFF)

seta sv_maxRate 9000
// Allow players to pull up to 9,000 bps

seta sv_fps 20
// Process 20 frames per second

seta sv_maxping 200
// Players must ping below 200 to connect

//CLIENT CONTROL

set sv_maxclients 16
// Maximum of 16 players on server

set sv_privateClients 3
// 3 of 16 slots require a password

set sv_privatepassword insert_your_private_password
// the password for the private slots

//GAME VARIABLES

seta timelimit 20
// Games will run for 20 minutes
// Use for Objective maps

seta fraglimit 0
// Games will not end based on frags
// Use for Death Match maps

set g_gametype 4
// Type of game the server will host
// 1 - Free for All
// 2 - Team Deathmatch
// 3 - Round Based
// 4 - Objective

set g_teamdamage 0
// Friendly fire is off (1=ON 0=OFF)

set g_inactiveSpectate 30
// Players become spectators after 30s of inactivity

set g_inactiveKick 60
// Players get kicked after 60s of inactivity

// MAP LIST - The list of maps in order that the server will run
// If you change the gametype to something other than Objective,
// don't forget to change the maps (i.e.: dm/mohdm1) as well
// Do not remove the "" as the maps will not rotate without them.

seta sv_maplist "obj/obj_team1 obj/obj_team2 obj/obj_team4"

map obj/obj_team1
// the first map to run

// TDM/DM Round Based Maps
// mohdm1 Southern France
// mohdm2 Destroyed Village
// mohdm3 Remagen
// mohdm4 The Cross Roads
// mohdm5 Snowy Parks
// mohdm6 Stalingrad
// mohdm7 Algiers

// Objective Maps
// obj_team1 The Hunt
// obj_team2 Rocket Facility
// obj_team3 Omaha Beach
// obj_team4 The Bridge