Now (winter) is the perfect time, while your tree is dormant. It will probably be starting to bud early in March.

I just planted two of the fruiting Amelanchiers (Saskatoon) today Barbara. I think its a good idea to do it asap as Sheila says...but not during a period of prolonged frost. We had 6C today, so a good time to do some winter pruning.

When you said that you had an Amelanchier as a bare root, I believe that it was meant to be used as hedging or as a shrub and not a tree. I am of the opinion that most Amelanchiers that are grown as trees would be grafted and trained as a single stem early in its growth.