If there is a difference between Qty on hand and Qty owned that means you are using Delivery Notes and Goods Receipts.
And you also mentioned that you don’t understand this system well () then i would suggest Delete all delivery notes and Goods Receipts. And then check Also act as Delivery note / Goods Receipt on all of your Sales and Purchase Invoices. (You can do it for all through Batch Recode).
Make sure you do this on a Backup file and see if those results make any difference.
I suggested this because i assumed you won’t need Delivery Notes and Goods Receipts, and you need just basic features of the program so you dont get confused.