I was trained to press them gently down to alllow the glitters to flatten, with my finger - very gently so that I did not introduce any oils from my fingers. or fingerprints !! Then 2 top coats of normal gel top.
I am sure you will get other replies from others that may also help you out.
I use a brush set aside for glitter to gently press the glitter in as RosieR describes, then with chunkier glitters I wipe off the inhibition layer after the first top coat,
And gently buff so any bits of glitter sticking up are levelled off, then apply another top coat and this usually works.
Obviously it depends what brand you're using and what products they offer, but I'm using INK London and if I'm needing more of an encapsulated effect I use their Clear Flubber on top of things like dried flowers, chunky dots etc, refine if necessary, then top coat but the draw back is longer removal time. (Not so bad with an efile though)