I just installed blogengine.net i never used it before. I downloaded some themes for my blog but can't find any place in control panel where i can install the thems automatically from cpanel
Go to "File Manager" then "public_html". Click on the folder icon for "wp-content" and click on the folder icon for "themes" and upload and activate your new theme.
Its a bit overdue for a reply to this question but another way is to simple FTP the new theme folder to the 'themes' folder of your blogengine setup. The theme will now appear under settings> Theme and you can simple select and save