You will need two things to get started. The first is the name of your comic, the second is the FTP password for your comic.
You should have two passwords - one is your forum account and password, the other is your ftp username and password. If your comic is mycomic.comicgenesis.com then your ftp username would be "mycomic". If you do not have or do not know what your FTP password is, then go to
this page in the CGWiki for instructions on how to get one (under "ftp password").
Once you have that information, you should be able to get started:
First, start Filezilla. Go File > Site Manager.
In this window, select "New Site" and give the site a name (I suggest the name of your comic to avoid confusion). Then enter the following data into the various options:
Host: mycomic.comicgenesis.com (replacing "mycomic" with the name of your comic)
Port: leave blank
Servertype: choose "FTP - File Transfer Protocol" from the drop-down.
Logontype: choose "Normal" from the drop-down.
User: mycomic (obviously you'd put the name of your comic, like in "Host" above)
Password: the FTP password you chose earlier.
Account and Comments leave blank.
To make life easier for yourself, click on the "Advanced" tab and in the box marked "Default local directory" use the "browse" button to find the folder you have all your comic stuff on your computer. You can skip this step if you want, but it'll make things easier for you when you want to upload if you have several drives or lots of folders (or several comics).
Once done - click "Done" to save your changes. To connect, under the "File" option you should see a little logo of a computer with a down-pointing triangle next to it - if you click on that triangle it should give you a drop-down with the site you just saved - click on that and it shoud connect you to your account.
That should be enough to get you started - feel free to ask if you have more questions.