Custom post types, custom fields (aka post meta), and custom taxonomies are all stored in the standard WordPress tables.
Under the hood Toolset uses normal WordPress functions such as register_post_type and update_post_meta to store data.
Toolset creates a number of custom tables to store post relationship data (readily identified because they are named with toolset), or maps caching data, but these should ordinarily be accessed via the Toolset APIs rather than directly.