Here is what I did.
First I went into dosbox straitup and had it writeconf.
I then copied the generated config file to a txt file named after the game for which I want to play.
Then I create a shortcut to dosbox with the following line:
"path\dosbox.exe" -conf AlienLegacy.txt
NOTE that my dosbox is not installed in a "long" directory so I can get away without quotes. AlienLegacy is the name of the config file, the extention of txt is just to make editing easier for me. Also that is the name of the game I am playing most.
Inside the config file you can setup the dosbox to work how you want such as cpu cycles, ram, frame skiping, screen filtering, and most notably where to send mt32 midi data. I say most notably 'cause I have y-sxg50 for midi so old midi sounds NICE.
At the botom of that config file is where you have an "autoexec.bat" section where you can create a batch just for your game, below is a copy of my "autoexec.bat" for alien legacy:
mount c e:\virtc
mount d y:\ -t
c:
cd\sierra\alien
al
exit
the first 2 lines mount the nesisary folders, the next 3 lines change drive letter and directory and then run the game, the last line (exit) closes the dosbox after I closed the game making it have a self contained feal. Now if only dosbox would pause emulation when it looses focus (optional).