Just as a discussion point, you can probably use a variety of things for coring. I say "probably" because I don't know how large the area is or exactly where it is located. But presuming it is small and more or less in the middle of the field (that is, not at some critical junction point or etc), you could use plywood or balsa or potentially foam coring. The core isn't totally unimportant (it needs to have a good bond with the upper and lower fiberglass/epoxy, for example), but it's mostly a spacer to hold the fiberglass skins both apart (distance) and together (epoxy, etc.). Depending on the size of the holes, you could also possibly fill with thickened epoxy (in stages if larger, so as to avoid excessive heat buildup).
Whether or not you want to glass over the top depends on the size of the hole in the top skin. If it's more than 1/2" or so and you only used epoxy (or other resin), without adding a new upper skin, then you could get outline cracking later.
If you are glassing over a slightly larger area, then you want a certain amount of overlap with the existing glass. In areas where flushness doesn't matter, it can be achieved by simple overlap. In areas where a final flush-with-the-original-material surface is desired, then you grind a taper into the existing glass. Around 12:1 ratio to the thickness of the glass skin of the area you are filling. So, for example, a 12" diameter hole in a 3/8" thick (solid fiberglass) hull would have a 4-1/2" taper.
When adding back the fiberglass you will generally use more than one layer, cut concentrically. In that case, I like to use the largest layer first, then taper to the smallest piece on top, especially when building to flush final surface. That way when you sand and fair, you won't cut through the largest, "best" layer as it will be safely on the bottom, with full adhesion. To get the shape of the glass pieces established, I lay down a piece of clear plastic and mark the outline of the patch shape in sharpie on the plastic, then cut it out to use as a pattern.
That may be more than you needed/wanted to know. Anyway, you may not need to exactly match the coring, material-for-material, depending on where the repair is to be made and how large it is. If larger, then you have similar stress characteristics and etc. to think about, but I'm guessing your repair may not be that large.