If you don't have reduced your pieces to some known sets, then I'm afraid, you have a lot of manual labour to do in order to create your initial list of elements you own. One tool that could somewhat help with that is BrickStock.
This guide on Rebrickable explains how you can import your elements into inventory. If the app you use could create TXT/CSV file of all scanned elements (it would be best if identify and store part ID, rather than names), the following option available on Rebrickable could be used:
Choose a file or external site to import from. You can manually create
your own parts file if you like, the easiest is probably a CSV
formatted file with appropriate headings. Rebrickable will
automatically detect the columns as long as you use the correct
headings (in any order): Part, Color, Quantity. For example:
Color IDs can be found on Rebrickable as well.