I can now see the image you posted at
http://nodexl.codeplex.com/workitem/22276. It looks like you have a number of collapsed groups, along with a bunch of ungrouped vertices. You say that you want to lock the collapsed groups in place and lay out the ungrouped vertices.
I'm afraid I have only a partial solution. First, to lay out the collapsed groups, if you haven't already done that manually:
1. Select NodeXL, Analysis, Groups, Select All Groups.
2. Select a layout algorithm at NodeXL, Graph, Layout.
3. At the top of the graph pane, select Lay Out Selected Vertices Again. It's hidden in a drop-down menu, below "Lay Out Again." That will lay out the collapsed groups using the selected layout algorithm while leaving the ungrouped vertices in
Next, to lay out the ungrouped vertices:
4. Right-click the graph pane and select Toggle Selection. That will select the ungrouped vertices and deselect the collapsed groups.
5. Select a layout algorithm.
6. Select Lay Out Selected Vertices Again. That will lay out the ungrouped vertices using the selected layout algorithm while leaving the collapsed groups in place.
This is only a partial solution, because the positions of the collapsed groups will not be preserved if the workbook is saved and reopened. You can lock the ungrouped vertices in place before the workbook is saved, but you cannot currently do the same
for collapsed groups.
If this sequence doesn't work for you, tell me which step is failing (apart from the save/reopen shortcoming I noted). It worked for me when I tried it.