Where exactly are you biking to and from? I work in Milton and commuted for 6 months to south east Mississauga. Depending on where in Milton you are starting from can make a bit of a difference. I used to ride out of the town on Main St, south on 5th Line which turns and becomes Lower Base Line. You can take that east across to 6th Line. 6th Line goes straight down to the QEW, there is an path under the QEW and then you can take Cross St/Service Rd to Chartwell, Chartwell down to the Lakeshore and then your golden into Toronto.
This route depends on when the bridge work on 5th line/Lower Base Line is done, currently there is no access in that area. YOu can jet across on Britannia Road to 6th Line and down, or Derry Rd over to 6th Line. Derry is two lanes each way now, but busy. Britannia can be busy with only one lane each way as well. Its a short 1.5km section.
http://ridewithgps.com/routes/450930