I'm sorry, but I've got bad news for you. The Mercedes-Benz navigation system that is integrated into your 2006 SL can't really be upgraded and it's also not the easiest system to replace. Map data can be updated with newer navigation disks, but it seems that you've already tried that with little luck.
Under normal circumstances, I'd suggest that you chuck the stock system and replace it with a more reliable double DIN unit, since you seem to want something more integrated than your TomTom.
However, the integration of the M-B COMMAND system with other vehicle functions would make removal of the OEM system difficult. Even if you did succeed in removing the OEM nav, there's the potential of crippling other systems (such a handsfree calling or climate control systems). Steering wheel controls and the COMMAND controller would also be rendered useless without special connections.
To make a long story short, unless you want to sink lots of time and money into a custom install of an aftermarket nav unit with better mapping, you're probably stuck with the TomTom.
I have a 2006 Mercedes SL500 Roadster. The COMAND nav system is crap! It's the software DVD which even if you buy the latest has huge areas without mapping. I live in WA. & only major roads are mapped. Anyone know if this system can be upgraded just use the screen & sys unit but run in better software?
For a car that was over $100k new I use a TomTom. Looks ridiculous but it works.