You can connect to GoodReader from any web browser (like Internet Explorer, Safari or any other). You will be able to upload files to your iPhone and create directories.

However, it is not the best way of doing this. You have to upload your files one-by-one. If you want to have full control over the process (to transfer whole directories, copy, move, rename and delete files and folders, etc.), you have to connect your iPhone as a network folder to your computer (what we call a "professional" transfer). See professional transfer at Step 6 of WiFi File Transfer manual for instructions on how to connect your iPhone as a network folder on various operating systems.

But if you have small number of files, uploading them via a web-browser will do just fine.

File transfer instructions: