You can freely load data into your Segment Warehouse to join against your source data tables.
The only restriction when loading your own data into your connected warehouse is that you should not add or remove tables within schemas generated by Segment for your sources. Those tables have a naming scheme of
<source-slug>.<table> and should only be modified by Segment. Arbitrarily deleting columns from these tables may result in mismatches upon load.
If you want to insert custom data into your warehouse, create new schemas that are not associated with an existing source, since these may be deleted upon a reload of the Segment data in the cluster.
We highly recommend scripting any sort of additions of data you might have to warehouse, so that you aren’t doing one-off tasks that can be hard to recover from in the future in the case of hardware failure.
If you have any questions, or see anywhere we can improve our documentation, please let us know!