Determine the optimum number of your users to migrate at a time. Your optimum migration group size will depend in part on the volume of data per user on the server. Migration group size should be correlated to the size and availability of your enterprise help desk, since you can assume that at least some percentage of users will call the help desk for assistance.
Your first few migration groups should be smaller than your expected optimum size, since these first groups will likely expose any unforeseen issues with documentation, your communication plan, and so forth before a larger group would generate correspondingly larger consequences. The first few smaller migration groups will also help you predict the demand on your organization's help desk upon the later migration of larger groups.
Finally, it is usually helpful to migrate users in logical groups, related by business function or by administrative entity or proximity, so they can support one another through the process.