Retaining permissions - SFTP over SSH /compression problems

I was having difficulty updating my website the other day. And now I realized why. All of the permissions in the uploads were changed. Never had this happen before with the old versions, so I didn't expect it. 12 hours of work and having to drop my database oodles of times. Can anyone here explain in very simple terms how to make uploads retain the permissions of the files and folders?

Would it be secure just to use zipped folders in c-panel file manager instead? I noticed that zipped items retain their CHMODs. And I can't find any way to compress files via smartftp. I don't have the compression option available under transfers. ... -f192.html

While I am at it. I bought the really expensive professional product, and it won't let me use terminal over ssh. What is wrong? I paid a whole lot of money for a souped up professional version. Even then, I would imagine something that you can get free from other folks would even come with your lowest version. So maybe mine isn't working right.

What about the permissions and zipping? Is Cpanel file manager secure? Or does it use FTP? I really need to know since I am trying the upgrade again tonight.

Where is the zip function that I can't locate?

How do I make it retail permissions?

The terminal is only available in the Ultimate Edition:

Well then I guess this leaves me with a little buyers remorse. Since now I have to use Putty anyways after spending nearly $60. A "professional" product should contain the minimal functions. There is nothing professional about this. If I would have realized that your professional didn't even have the basics, I would have moved on.