To write text to a file, you can use one of the procedures described here:
http://msdn.microsoft.com/en-us/library/microsoft.visualbasic.fileio.filesystem.aspx
To include quotes in a string literal, use the Chr function, or double up on the quote marks:
Dim CmdLine As String = " /c Echo mkvextract tracks ""%SystemDrive%\Videos\Temp\Video\MkvD_Video_Temp.mkv"" " & VIDMkvD & ":" & VOtPtMkvD & " " & AIDMkvD & ":" & AOtPtMkvD & ">> ""%SystemDrive%\Videos\Temp\Jobs\MkvMakeFileD.bat"""