A better idea would be under iw-home/httpd/iw/, e.g. iw-home/httpd/iw/custom/your.css. The httpd/webapps folder is not meant to be touched directly ever -- that's what the UITK is for, and having to execute a make_toolkit rebuild to update a CSS file is just plain silly. The httpd/iw folder was meant for static web assets (JS, CSS, IMG, etc.) for use within the TeamSite UI, exactly like yours.