First, you'll need to make sure that you've created and installed your "In-House" Distribution Certificate via Apple's iOS Provisioning Portal.
Open your Project Options in MonoDevelop and navigate to the iPhone Bundle Signing section.
If you've got MonoDevelop 3.1.0 or later, you'll be able to set your configuration to:
Otherwise you'll simply have to select your Provisioning Profile manually.
Once you've selected your signing certificate and provisioning profile, click the OK button to dismiss the Project Options dialog.
In MonoDevelop, click on the Build menu and select Archive. This will build your project and archive it in a location that Xcode will be able to see it in its Organizer window.
Launch Xcode and then click on the Window menu and select Organizer. At the top of Xcode's Organizer window, you will see an array of icons. Click on the one labeled Archives.
Find your application in the list of archives and select it.
Now click on the Distribute... button in the top-right area of the window and select Save for Enterprise or Ad-Hoc Deployment.
The next screen will prompt you for your code-signing certificate, providing you with a drop-down menu listing your available options.
Clicking Next will cause an action sheet to slide into view, prompting you for the location to save the AppName.ipa package and the AppName.plist file.
Important: Make sure to toggle the Save for Enterprise Distribution checkbox.
Once you've finished filling out all of the fields, click on the Save button.
You'll need to upload the saved AppName.ipa and AppName.plist files to your corporate web server in the location that you specified in the previous step. You'll also need a web page that will link to your app using a hyperlink similar to the one below:
<a href="itms-services://?action=download-manifest&url=http://internal.mycompany.com/Applications/AppName.plist">Install AppName!</a>
That's it! You're done!