If I have a form which is based on a Query and is using 3 different tables, how would I go about updating specific records from the form into a specific table?
This in itself should not prevent you from changing the data in the underlying tables. You must be doing something else in your query(s) to prevent you form updating the data. Sometimes summing or total a field will do this.
With out going into to much detail, I would suggest you do a new form that will be used to update data which is based on data from the first form, using the original form as sort of a look up form.