You can actually put the file anywhere inside your "Scripts" subdirectory without any issue, and it'll work as intended.
When you see "Add to your Customs folder" in custom packages, it usually refers to most people having created a folder called "Customs" or "Custom" within their Scripts directory, and keeping any non-"stock/distro" RunUO/ServUO releases in there. The reason was typically because it's easier to find, and back when you had to merge any changes to the emu in by hand, having everything separated like that made life much easier. With the advent of Diff tools and Git/SvN auto-merging, this practice is not only outdated but highly unnecessary due to the functionality of auto-merging when updating your distro/core files. Those that still do keep custom stuff separate, would only really be doing so for aesthetic or organizational purposes (me included). Hope that explains it for you!