Solution 1:

Use the route command to show your routing table. Typically, your computer will have a default route (possibly the last network interface added) through which all your traffic will be routed.

The default route will have a destination of 0.0.0.0 or maybe just the word 'default'. That's where your traffic is going through. You can change it with the route command also.

http://www.cyberciti.biz/faq/linux-setup-default-gateway-with-route-command/

It may be possible to configure individual programs to bind to different network interfaces.

You may also look into bonding your network interfaces but I have never tried it.

Solution 2:

This is an answer to similar question.

To download files by a specific route you can use Wget: wget --bind-address=<localIP> <file>, where <localIP> may be either your 3G (external) or company (internal) IP.

Route metrics can be set through NetworkManager (the tray applet).

Also this howto explains how to set routing policy to work for multiple Internet providers; you'll probably want to create a post-up script for 3G PPP interface that would set everything up.