I keep most of my code clean in that area so when I add them I don't seem to have a problem. saves time for me having to keep track of the remote scripts I have loaded in case a specific alias isn't there. For big aliases though, then i'll keep them added as a separate remote script though.
I create my own little seperators by starting a line off with a comment semicolon.
something like
;--------------------------------------------------
works for me to separate my aliases into categories if needed, but I only have one of those separators now.. seems a bit unorthodox but it does help me visualize a separation between my needed aliases and my custom ones lol