I don't quite understand why the glue spots are visible through the paint. In any case, though, I find that one of the most useful tools for 1/700 ship modeling is a bottle of PolyScale clear flat. It's as thin as water, and if applied with a small brush becomes virtually invisible within a minute or two.
The only potential problem is that if you've put any parts on the model with white glue, the clear flat may soften it up. In a case like that you'd probably be better off with a solvent-based flat finish.
If you don't have access to PolyScale, I suspect the Testors Acryl clear flat is just about as good for the purpose. PolyScale just happens to be the one with which I'm familiar.
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