If you make a gzipped tar file, you can upload that and it will be unpacked automatically. That is how I usually upload several files at once.
Our course is hosted on the MAA servers, and they don't provide ssh access to those, so no, you don't have command-line or sftp access to the course. If you ran your own server at your own college or university, you might be able to arrange for that.The mechanisms that I know all rely on having a full WeBWorK installation, and I don't see an easy way to avoid that. I suppose it would be possible to make a command-line script that pulls in the required components of PG and WeBWorK that would compile the problem and return any error messages, or would allow you pass a collection of answers to pass to the answer checkers, and would return the results, but I don't know of anyone who has done that outside of a full installation with a server backend for processing the problems.