Look at the bottom half of this link. It shows the reverse direction.
http://www.orioshuttle.com/_eng/pdf/OS_03_ENG.pdf
EDIT: the schedule shows both M-F and Sa-Su times (much more limited)
When it says APT that is the stop at the airport. It departs from terminal 1and 2 at Malpensa. The journey takes 2h. The shuttle runs about every 2 hours. It looks like the 11 am shuttle is the first one you might have a chance to take. It would get you to the Bergamo airport at 12:40.
Personally it sounds like a very tight squeeze to me getting from MXP to BGY in your time frame. Do you need to check into your BGY flight 1-2 hours prior to your flight? I'm assuming that the BYG flight is a separate ticket. Have you priced what a ticket purchased on the spot at a later time would be as a backup plan so you don't stress out?