Hi.
Transparent mode would be the easiest to implement in an existing network as no re-addressing is needed, and since it acts like a bridge. you can also control non-ip based traffic (which routed mode can't).
Routed mode however has some more features which don't exist in transparent (like multicast routing, routing protocols etc...). so if you don't need any routed-mode only specific feature, stay with transparent.
With transparent you have to be carefull how to implement it so as not to cause layer 2 loops.
However since the cat6k routing features are a lot more advanced than the FWSM, i'd say keep the routing to the msfc, and let the fwsm just do firewalling. so best to use FWSM in transparent mode.
The fwsm config guide section about the 2 modes, explains the difference between both, so i recommend you read it and based on your requirements implement what you want:
http://www.cisco.com/en/US/docs/security/fwsm/fwsm41/configuration/guide/fwmode_f.html
Regards,
Fadi.