It's best to store your skin specific scripts with the skin. When you use the AddToCombinedScript parameter, it keeps there from being yet another file downloaded by the browser.
To use the script loader to load your JS with the combined site script, do the following:
- Create a new js file in your skin directory, I usually name it skinscript.js.
- Add <portal:SkinFolderScript ID="sfs1" runat="server" ScriptFileName="skinscript.js" AddToCombinedScript="true" /> to your layout.master. I usually add this right after the <asp:ScriptManager control.
You can move the scripts in your layout.master to this new js file but it may take a little bit of trial-and-error because depending on how they were written, they might not work properly being lumped together. We always add the toolbar and superfish scripts to this file and we don't have any problem with them.