I don't know about the Logitech software or specific features of the 
Harmony One. For specific help on topics regarding these, please 
contact Logitech. I don't own either of them and thus can't offer any 
help there. Sorry.

But if you can get the Logitech hardware to send the IR codes you want 
in the places you want, the solution should be easy:

What you may want to try to achieve is this:

1) have the Harmony One sending the codes recognizable by the Keyspan 
receiver - namely from the Apple Remote and Keyspan Remote.

2) use the Apple Remote button codes for navigation and general 
purpose remote control

3) use the Keyspan Remote button codes to launch individual 
applications.

You achieve (3) by going to Prefs > Mapping > Global mapping and 
selecting the respective applications you want to launch (by selecting 
the corresponding "Behaviours > Activate .. Behaviour" action in the 
action chooser popup for the button) to the respective Keyspan 
Remote's buttons. Now, when your universal remote sends the respective 
code, Remote Buddy reacts accordingly.

Best regards, 
Felix Schwarz