While I like ccccchunts recommendation of stabilizing, I don't yet have all the equipment for that. Something I have started doing, and would do regardless, especially if you have some materials that are particularly hard (very hard hardwoods, metals, etc.) compared to softer woods, is to put some sanding paper on something flat and hard, and sand with that.
I have been using batches of those very large popsicle sticks, with strips of various grits of sandpaper, glued with contact cement. Each side of the stick has a different grit, and I have every grit from 400 up through 3000. The 400 grit stick has two different kinds, one non-wet that works REALLY well on most things on one side, and a wet/dry that works well on certain things and is usually better for resins. Then the rest of the grits are all distributed onto both sides of other sticks. I'll get a photo of my sandpaper popsicle stick sets tomorrow, if I can.
Anyway, having a hard, flat surface can help you make sure that you don't end up with peaks and valleys across softer and harder materials in a hybrid blank. I find its most useful when I create blanks with metals in them, but it is also useful when you say combine really hard woods, say katalox or lignum vitae or ebony, etc. with softer woods like maple. You usually get nice clean transitions across each material.
I've not been able to master this yet myself, but another option is to truly master using a skew, to the point where you can turn such a surface that you don't need to sand at all. I have only a couple of months overall under my belt with a skew, so I certainly cannot do this yet. I've seen some pens shared by other members on this forum who do that, and they can indeed look excellent. For some combinations of woods, turning this way would less prone to issues than sanding, as often sanding will leave you with alternate colored dust clogging the pores of other woods. For example, padauk with maple...your maple will pick up and hold the red sanding dust from the padauk. Walnut can capture lighter sanding dust in its pores. Stabilizing can help with that as it fills the mores and effectively seals the wood, but I suspect the best way to avoid it, is to not produce any sanding dust at all.