If your recordsets are a one to one correspondence, you can sort them both by the foreign key that links the two tables. This will ensure that the results are in the same order, so that the first record matches with the first record, second with the second, etc in the two recordsets. If this is the case you can then have a loop that steps through both recordsets at the same time and inserting the code to check the checkbox if needed.
If they are not one to one correspondence, you will need to use two loops to process the information. The first loop will step through one of the recordsets and an inner loop will loop through the other recordset for each record in the first recordset. In the inner loop, you will check for if there is a match and if there is you will insert the code to check the checkbox. Make sure you remember to set the second recordset to start back at the first record in the recordset just after the inner loop.
Hope that helps.