R-6 download connection

I am currently doing training here in Johnson County , KS. They will have over 800 R-6 AVTS units. For the upload process, we have 2 digiboxes, a 16 port connected with a 8 port, which has 24 modems attached, which is fine. However, for the download process, will we do this process via modem also??? For all of the certifications and demos that I have done in the past, I have only done a serial connection from the Host to the R-6 unit. If I do the serial connection, that would mean that I will have to change my setup on the Host computer each time I do a download, and then set it back to modem for upload.