What's the best way to add events to the calendar? Do I have to change the HTML everytime I add an event if my calendar is already online? I'd like to be able to add the new events and upload them without changing my code or adding new files. Is this possible?

If you're only adding events, not changing the calendar size or other settings, you should be fine just saving & re-uploading through the program without editing any HTML files.

How does the upload feature work? When I make changes and save them, I click 'upload'. There's nothing in the bottom 3 boxes (host folder, local folder, comment). I click 'connect' and it says 'upload files here'. There's nothing listed in the server directory. What am I doing wrong?

Hmm..well, are you sure you have the right login (FTP) settings? For most servers, you can leave the bottom 3 boxes blank. For some, you may have to specify a remote host folder, or you can use that out of convenience to jump to the right folder w/o having to navigate to it each time.

When you hit Connect, though, it should list your remote folders/files in the box. If it's blank, I'd either re-check the login settings entered or see if any firewall software might be blocking the connection.

When I add events I choose save and it tells me this file already exists. I choose to replace it. Then I click 'upload' and the box comes up. In the left pane it shows my root directory. Now the entire right side is grayed out and blank. I can't add anything. I'm using a trial version that has 4 days left. I want to make sure everything works well and then I'll buy it. Any suggestions on the upload problem? The right side wasn't grayed out a couple days ago.

Weird, I never seen any part of Calendar's upload where it shows left & right panes where part would be grayed out. Unless you mean the list of servers to connect to and the right side containing the login settings.
http://www.coffeecuphelp.com/adam/images/Cal_Upload.jpg

Yes, the login settings are grayed out. The Server Directory list that you show has nothing at all in it.

When I first downloaded the program the login settings weren't grayed out.

Ok, it's gray for me until I click the Server I added on the left side (My Sites), then the settings show up. If there's no server on the left side, you'll have to add one.
http://www.coffeecuphelp.com/adam/images/Cal_Upload2.jpg
http://www.coffeecuphelp.com/adam/images/Cal_Upload3.jpg

OK, now when I click on my site name in the left column the right column isn't grayed out. Everything's filled out except the last three lines. When I try to upload my changes there's nothing showing in the server directory box. It doesn't make any changes to my online calendar when I click 'upload files here'.

Now we're back to our 3rd & 4th posts in this thread.
Does it say Connected or Disconnected on the bottom left of the box with the "Upload Files Here" button? If the login info is correct, my only guess would be to try disabling any firewall software (temporarily) to see if that's blocking the connection, and to tell the software to allow Web Calendar if that's the case. I always have Passive Mode checked, but when I unchecked it, Windows Firewall popped up and asked if I should Block or Unblock Web Calendar. If you have anything else like Zone Alarm, Avast, or McAfee Firewall (or Symantec/Norton), I'd look into those settings.