Journal Entries for most anything in QB are Errors. They are violating cash Vs accrual basis reporting; they cannot use Items or Names correctly; sales taxes are not going to calculate; you cannot do this with Inventory, etc.
That person is so very much making a mess of this data file.
Yes, you Should be using the other tools. This program has an Interface = tools. Look at all the menus and the options; that is WHY they exist.
JE are mainly useful for Year End depreciation and similar Non-Name, non-Item, non-Banking, Non-AR and AP, non Calculating, Non-Qty- related, purposes.
Show them the issue: Run a Sales Report, or a Job Profitability report, or an AR Aging Summary report, or an AP summary report. Let them see the issues.
Here are the Video Tutorials for how to use QB properly: