You can add the .dll to the 'mcc' command with the -a flag. Also in the matlab code you will have to modify the location relative to the ctfroot. Here is an example that can be used as a reference.
imaqregister(fullfile(ctfroot,mfilename,'filename.dll'));
Also if you are using 'deploytool' to create the standalone you can add the dll in the files required for your application to run section. Here is a link that talks more about path management in deployed applciations.
I hope this helps.
