I created my start panel with a slight drop shadow and transparent sides so that it wont be completely touching the side of the screen when applied. So the sizes of the various parts (Userpane, Programs, etc) will include the actual start panel aswell as the drop shadow and transparent sides (as shown in the image that I posted earlier). So I'd rather not use the method you mentioned about "no blank space around the sides to deal with."
Basically, here's how I do it:
I draw the entire start panel (with drop shadow and extra room around it so that it doesnt hug the side of the screen when applied). Then I merge visible so that the entire panel and shadow are one image. Next, I set the guides for each of the 5 sections. Here's where some of the problem occurs --- I used to use the rectangle tool to select each part one at a time (say, the userpane), I would then copy (also tried copy merged). Then I'd open a open a new document and paste it there. The problem I found with doing this, is that the new document canvas size is only as big as the image piece but it DOESNT include room for the transparent edges (which I want). SO,I've recently been taking a different approach:
After creating and merging the startpanel into one image on one layer, I go to Channels Tab, create a new Alpha channel, and make it active (so that the entire document looks black, Then I select the section (say, the userpane again), copy the Alpha selection of the userpane in Channels, open a new document, I then de-activate the Alpha channel and go back to the startpanel layer in the Layers tab on the Start panel document, Copy that, then paste THAT selection into the new document. But it pastes the userpane selection in the middle of the new document. So I nudge the image to the edge of the side where it would meet with the other sections (in this case, I nudge it down a bit to match up with where the tops of the programs and Places List would be; careful to nudge it just to the edge and not beyond that. Doing it this way allows me to keep the same width and height of the selections from the original startpanel image including the "blank" areas (which I want to keep). But...... like I said, this method must also be flawed because when I import the 5 parts into SKS, they dont seem to match up evenly (EVEN THOUGH, all of the dimensions of all of the five sections DO add up to the dimensions of the entire original startpanel (which includes the "blank areas").
I'm thinking that the guides might be causing the issue. Here's my theory:
After setting up the guides to where I want the sections to be cut, using the rectangle tool (set to snap to guides). I think that when the rectangle snaps to the guides of each selection, perhaps it snaps to 1px INSIDE of the intended selection (thus, causing the selection to actually be 1px smaller that what I want) OR that it actually snaps to 1px OUTSIDE of the selection (thus, causing the selection to actually be 1px larger that what I want). If either one of these theories is correct, then the image sizes would be inaccurate.
My last method to solve this issue is to:
After setting the guides, I use the rectangle tool to select one of the parts (userpane), then crop it so that it preserves the "blank" areas, and I save it as Userpane.png. I then undo the crop, select the next part (say, programs) using the rectangle tool again, crop, save as Programs.png. I do the same for all five of the startpanel parts. I haven't imported the images that I did using this method into SKS yet. But I will post the results once I do.