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Generally all it takes to solve this is some planning on the paint scheme.

What I do is paint everything that is going to be matte finish first.
Then I apply the varnish (Usually spray, but also would be the step to brush it on).
After that dries, I will paint any parts of the model that need to be metallic or glossy.

Having different parts be matte/glossy can look bad, but done right it can be very effective. A female "cheesecake" model in fake leather boots, for example. Paint the body/legs with the matte varnish, then paint the boots the glossy black/whatever.
It really makes the metal/glossy parts of the model pop.