You can change the data connection mode via the Site Manager on the Options tab.
Data Connection Mode
Use global settings
Passive mode (PASV)
Active mode (PORT)
In most cases changing between passive and active mode will have little impact on the speed however some users have reported faster speeds using one over the other.
Using active mode can be more difficult than passive mode because it requires the FTP server to connect to your computer, this might require configuring your router and setting up port forwarding rules.
If you're experiencing slow uploads and using Windows XP you might want to checkout this post
http://www.flashfxp.com/forum/flashfxp/faq/15895-%5Bsolution%5D-slow-uploads-windows-xp.html