Each app has it's own file space so that Safari can not browse for files to upload. The result is that the Choose File buttons on most sites are grayed out to show that you can not do this in Safari. Is a good security feature as far as preventing viruses, trojans, and such, but it does make for inconveniences on occasion.
There are a few workarounds.
If the site you need to upload to can accept URL addresses as and alternative method to upload, then get DropBox and place your file the public folder there. You can either use the DropBox app, or GoodReader to upload/download files from DropBox. Lots of other apps also have direct DropBox support. Once in DropBox's public folder you can get a URL and use that to copy the file to the other website.
This method can be used with any online storage site, so long as it gives you a URL that ends in the file's actual name and extention. Sites that supply sharing URL's with weird non-file endings don't' usually work.
Or you can use iCab Mobile. It doesn't work with every site, so you have to experiment. You first use the Open In feature in your fist app to place a copy in iCab, then go to the site to do your upload and proceed as normal. It will either work, or give you some obscure error.