At least with the version of the Eye-fi software currently on my machine, you're limited to uploading to one home computer and one online destination. FTP counts as an online destination, so if you upload to FTP, you can't also upload to Picasa, Flickr, and friends without some hackery. Some folks on the Eye-fi forums have suggested Pixelpipe as a multiplexer for the online services,

I almost always want to clean up my photos before uploading them, so I just have it deposit them on my file server via FTP and do my uploading to Picasa using the Picasa desktop app.