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If you used wood flour in your resin and thats the material that you are referring to, which fills the wider spaced seamlines, then yes just go right over the glue line with the thinned filler stain and allow to dry thoroughly. Make sure you sand with a good fine paper and wipe down your surface with materials like Denatured Alcohol, which evaporates quickly and will leave little residue and check for any missed sanding marks before you stain.
But I would not glass over varnish though. You will need to use special coatings hardener for the wetout of the glass and then when you fill the weave with additional coats, you will then need to varnish over with a good UV varnish. Some folks do use a clear coat over the special coatings hardener. But do a test section and make sure that any varnish you decide to use will cure over the epoxy. There are some exceptions with some of the varnishes in regards to drying over some of the epoxies.
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