Organising and sharding your migration/transfer project is one of the most important steps when working on a migration process. We always recommend keeping it as simple as possible for your own sanity and have some tips on how we recommend organising things.
Run an organisation scan first
An org scan will give you a great overview of your entire dataset and can be used as the basis to begin splitting up your migrating and configuring mappings. See here for more details.
Map out your migration in phases
It can be enticing to try and do everything at once, if possible, use several projects and keep projects to a max of 1000 mappings.
Migrate top-level folders
Cherry-picking subfolders, while possible and useful in some cases can lead to accidental data loss. If you need to prune data, do it on the source before the migration and keep the mappings as clean as possible.
Test first and review warnings
Always run a pilot. A pilot migration, even just on a small folder will help you understand what the tool is going to do and will build confidence.