The basic architecture of SL (part of the reason it is as lightweight as it is) doesn't permit individual placement of icons, and devs have told us that changing that is not contemplated for the near future. There is a workaround, though, as long as you work within the parameters of how icons are automatically placed: you can create empty spaces by using empty folders to use as placeholders. (If you've signed up for the beta program, the latest beta release now creates folders that remain invisible until you add an app to them. The current "stable" release creates a folder with a folder icon, which can be replaced with an invisible icon using the Full Transparency SL Theme.)
The only thing you have to be careful of is moving invisible folders around: if you want to switch places with an actual app, you have to move the folder, and not the app: otherwise, the app will be placed into the folder.