Right or wrong, I always tell my clients to submit multiple applications as if they were going to be separated as soon as they're removed from the envelope. Send a separate check for each application. A separate copy of the Trust for each application, etc. I see no reason all the applications can't be sent in a single envelope, however.
My record is 6 applications in the same envelope. I actually sent that one certified mail with return receipt requested. Took right at 9 months--January through September, 2013.
Rod