Extrude From:
Current Face - Extrudes from the selected (green/yellow) face.
Marked Face(s) - Extrudes from all the marked (blue) faces in the room.
Extrude along:
Normal - This is the only one I really use, it extrudes the face depending on which way the normal is pointing.
Y-Axis - Forces D3Edit to extrude the face along the Y-Axis, helpful if you have an angled face to extrude straight.
X-Axis - Forces D3Edit to extrude the face along the X-Axis, helpful if you have an angled face to extrude straight.
Z-Axis - Forces D3Edit to extrude the face along the Z-Axis, helpful if you have an angled face to extrude straight.
New face normals should:
Point inward - All of the new normals point 'inward' toward the center of the room. This is used for creating the 'shells' of rooms.
Point outward - All of the new normals point 'outward', or away from the other faces. This is used mostly for creating pillars and pipes.
Misc:
Distance - This tells D3Edit how far away the second face should be placed.
Delete base face(s) after extrusion - This will delete the faces you are extruding from (or, in other words, the currently marked/selected faces). This is helpful if you are doing multiple extrudes or if the base face isn't visible to begin with.
Use these settings for default extrude - This will use your current settings as a 'default' of sorts. Then all you have to press is Ctrl+E and it will extrude using these settings without even showing you this window.