Just be aware that the solvent in the lacquer can loosen the stain, so brushing or wiping does have a tendency to move the stain around a bit. Not normally an issue on a single colour stain, but if you're attempting a sunburst, then you need to be very careful. One reason why spraying is preferred. Get the first coat on without working it in or repeatedly going backwards and forwards.

Once that coat's dried, then you're unlikely to move any stain around, so you can be more thorough.

If you've got any binding, then brushing lacquer with stain in can obviously discolour the binding, so either mask it, or scrape the first coat of lacquer off with a sharp knife if you notice any discolouration.