OK, this might get slightly complicated. Now, I'm guessing that your subform is showing the records you want to update yeah? What you need to do is create an update query to say "Update the check box where the records match the link criteria in the subform." So what you need to do is create your query in design view, using the table behind the subform. Drag down the check box field, and the fields in the table that the subform uses as a link. Put an x in the criteria of the link fields (I'll expliain why in a minute). In the "update to" bit of the check box field, put "true".
Now switch to SQL view. Copy the text. Go to your VBA editor, in the on click event of your master check box put "docmd.runsql" and paste your SQL code in. Now, look at the code, and where it says "WHERE [Link Field Name]="x"", take the x out and put your ink field name in.
Now, when you click on the master check box, it should update all the sub check boxes to true, and it should only do the ones that are displayed in the subform.