Which version are you using?
In 7.3.2 there is a 'description' text box to fill out when defining criteria which may be of some help to explain what the field is without using the database name.
I can help you with one of your points, which is renaming the database field names.
You can rename these by opening up the query in question in query and report designer and going to the criteria page, open the criteria you want to rename and you'll notice there's a 'Description' box; enter into there what you want the users to see.
Hope this helps.
As well as the advice you've already had, a couple of other things that might be of interest:
You can either display the criteria as a grid or a list - I'm not sure what your users would prefer but this option is on the last page of the query setup so you can try this out perhaps.
You mention "box where they can type values in the third column". If you are pulling through a criteria at the top level of the object then they will get a drop down values to pick from rather than having to type in the value. So using Status as an example:
- If you pulled Status.Name onto the query criteria the user would need to type in the name of the status they require.
- If you pull the top level of Status (don't expand Status just drag on the top level relationship) onto the query criteria the users will instead be presented with the list of possible status values when running the query.