If you mean, you have a design that features some parts that are scored and some parts that are engraved, just make sure to make things intended for different operations in different colors. I.e., red for scores (these need to be stroked, not filled figures) and blue for engraves (these need to be filled, not stroked areas) for example. Then in the GFUI you will specify settings for each operation (score, cut, or engrave).
If you mean, you have a figure that you want to both score around the perimeter and also engrave the entire center, you will need to do that in two separate runs. Just specify to score (or engrave), let the machine complete the job, then without moving your piece specify the engrave (or score) and restart the job. It will do the operation in exactly the same place as long as you have not moved the item.
Look in the Glowforge Tips and Tricks category of this forum for lots of Inkscape tutorials that will better explain all of this.