Yes, the file manager in cPanel can be problematical. Here is how you can get around the one file limitation of cPanel.
1) Using the cpanel file manager, upload the ORIGINAL zip file - NOT UNZIPPED - to your zen cart main directory - do NOT unzip it prior to upload The cPanel file manager sees the zip file as ONE file, so you have now worked around uploading all the files at once.
2) Once you have uploaded the zip file, select it, and then using the "Extract" icon on the top of your file manager window, extract all the files. When this is finished, you will have a new folder named "zen_lightbox-v1.6.2_20110220" (Note: you may have to hit the "Reload" button if you can't see the new folder, this will refresh the view in file manager) Navigate into this folder and delete these files:
_readme_files
readme.html
install.sql
uninstall.sql
upgrade.sql
3)You should now have ONLY two folders and one file:
images
includes
jscript_zen_lightbox.php
4) Using your cpanel file manager, click on "select all" and then on the left side use the "Move File" button and move the files up one directory into your main zen cart directory. At some point you will be asked if you want to overwrite the existing files, and your answer should be yes.
This will finish the upload part of your installation. You can now remove the empty folder and the zen_lightbox_1-6-2.zip file that you originally uploaded just to clean things up a bit.
Now complete your installation using phpMyAdmin from your cPanel as per instructions in my previous post. and you have completed your installation.