Add the AllowedUploadFileExtensions entry to your user.config file and modify it to include the type of file you want to upload. Below is the current default entry from the web.config file.

<add key="AllowedUploadFileExtensions" value=".gif|.jpg|.jpeg|.png|.flv|.swf|.wmv|.mp3|.mp4|.m4a|.m4v|.oga|.ogv|.webma|.webmv|.webm|.wav|.fla|.tif|.asf|.asx|.avi|.mov|.mpeg|.mpg|.zip|.pdf|.doc|.docx|.xls|.xlsx|.ppt|.pptx|.pps|.csv|.txt" />

Depending upon where what functionality you are using to upload the file to the site and what roles the user has, you may also want to be aware of the AllowedLessPriveledgedUserUploadFileExtensions entry in the web.config. I am not 100% sure where this is taken into account, but just wanted to mention it in as it may apply. The default value is below.

<add key="AllowedLessPriveledgedUserUploadFileExtensions" value=".gif|.jpg|.jpeg|.png|.zip|.pdf"/>

Oh, also remember to touch your web.config file after you modify/save your user.config so that the user.config changes are picked up.

Yes, if you create a folder via File Manager it is created on disk. It will be located in the Data/Sites/site-number directory of your mojoPortal install (or whatever sub-directory you may have decided to create it in).

If you can't locate the directory or file on the physical disk, if you go back to File Manager are you still able to see them there?

Are there any errors in the system log after you create the folder and upload the file?

Does the Data directory (and sub-directories) have the proper permissions set up so that mojoPortal can write to those directories?

Just trouble shooting questions to try and help without actually seeing what is going on.

Yes, you do need to provide the path to the file from any links.