Yes, you can continue to use your diatom filter while treating. It will have no impact on the chemicals you are using to treat, other that you will need to discard (change) the filter module after you complete treatment as it will absorb the medication used.
The diatom filter can aid inthe treatment of ich if used with diatom powder and a diatom filter pad-the ich organisms can actually be trapped in the diatom filter powder/filter where the treatment can have larger 'punch' as it continuously washes over any organisms held in the filter media.