This was then glued onto a plywood top.
This isn't what you asked about but you might want to stop right there. You will likely run into problems if you glued solid wood firmly to a dimensionally stable material like plywood. Some allowance for seasonal movement must be made or the wood will strain against the glue and can crack itself free or will bow or otherwise warp the board.
I'll edit this out later if the situation is not how I'm visualising it but I wanted to give you the headsup in case it is, as this takes precedence over filling gaps.
Do I use a mix of wood glue and cherry wood dust? Should I just fill with wood filler?
Yes :-) People do both very widely. Neither is perfect but both work acceptably well.
Wood dust and glue
When you mix conventional wood glue (PVA type, yellow or white doesn't matter) with the wood dust of the same species you will nearly always end up with a fill that is darker than the surrounding wood. The result is similar to the colour of finished end grain, so quite significantly darker.
I don't know why it is so commonly stated that this is "a good colour match" because it's not. You can get a good colour match if you are using hide glue, but obviously that's not the glue most modern woodworkers are using and many guides saying they're getting a good colour match aren't either.
Epoxy is worth trying, you can get a slightly better result using epoxy instead of PVA (slightly). It does allow you to progress much faster since most epoxies set hard enough to be worked well under the time a normal glue + wood dust mixture dries out, and the texture is usually smoother and more uniform. This is something I think is worth experimenting with, especially for larger voids, but with those I think they should be made a decorative feature and no attempt should be made to match the wood colour (I often go with a very dark brown or black).
Superglue or CA can also be used for some fills, but again, expect them to be darker. I use this myself sometimes for hairline cracks but I don't think it's really suitable for larger voids, in part because of the very fast 'drying' time. Such fills would also be very brittle which may be an issue the larger they get.
Wood filler
Commercial paste wood filler can work well, especially when you are not staining the wood (they don't tend to stain well). But be aware fillers vary widely in type and qualities, and it may be difficult to find one of just the right colour. But most can have their colour tweaked using dry pigments or with a little of a suitable paint (acrylic for waterbased filler, oil or enamel paint for oil-based) if you're up for some experimentation.
Note that wood fillers can, similar to end grain, go a little darker once the finish goes on. If the change is not too pronounced it's not a big deal, it is commonly advised to make fills slightly darker.
What's the best way?
As usual, there is no one best. There are a multitude of opinions on what makes the best type of wood filler and professional woodworkers and finishers each have their preferences, sometimes based on the species and final finish more than having a single way they will always use.
In addition to the options above people use a wide range of shop-made filler concoctions, at the more modern end of the spectrum spackle or drywall compound with wood dust and some commercial filler, and at the old-school traditional end linseed oil, wax and various resins coloured with dry pigments, softened using heat or with the addition of some turpentine.
Also at the traditional end but commercially made are shellac or wax fillers. Neither of these may be easily available to you but some people swear by them. Both can be melted into defects e.g. using a soldering iron, and then levelled off with careful scraping. Again these would traditionally be applied to the finished wood, allowing for a more accurate match of the colour of the surrounding wood.
