On deselecting polygons by material - if you have the space, open the Tool Settings pane. With the Polygon Seelction tool active that lists all of the polygon groups (actual groups, material zones and so on) with a + next to each to select it and a - to deselect - if you overflow when selecting then the unwanted material zone will have a solid - next to it and you can just click that to deselect the overflow polygons as randy did with the context menu, without needing to know the material name (and looking for solid -s can cue you to overflow selections in the first place).

On saving - in 4.5 save as a scene subset, not a full scene, or the default behaviour (when you double-click) will be to replace the current scene, rather than merge in (it will prompt you to save your current scene, so you won't lose work, and you can right-click rather than double-click to get Merge, but it's still annoying). You could also save the modified suit as a new Figure Asset (File>Save as>Support Asset>Figure Asset) but then you lose the compatibility info forsmart content, which may be annoying if you use that.