I dont really have any uploading tips beyond select the folder and tell the program to send it to the server.
you really just have to keep in mind what files are being updated and select them for uplaod.
ig you are making a change using the design view on a page, not any server behaviors, then you dont need to worry about other files.
if you are editing a server behavior, make sure to upload the folder for that product. In this case, you where modifying the Security Assist Rules, so needed to upload the security assist folder.
That's not really a hard and fast rule though. For example, with data assist, no files will get changed in the data assist folder when updating the insert record behavior.
but with Universal Email, 2 files are usually created in the webassist/email folder.
all of that is a long winded way of saying it's not a simple task to manage the files between your local and remote sites.