Can I migrate all my multiple AmeriCommerce stores at once?

Yes, Cart2Cart allows you to perform AmeriCommerce multistore migration. However, you need to ensure that each of your multiple stores is displayed on a “Multi-store Configuration” step of Migration Wizard. If not, most probably the Access Token you’ve entered has not rights to access some of the stores.

In this case, you need to edit your Access Token (Tools > Apps & Addons > API Apps & Integrations) by putting a checkmark in “Tokens Access All Stores” box.