Hey ShellDude!! Sorry for the delay, I've been busy catching up on life things the last couple weeks. After a solid year of CBT/Kickstarter the life stuff really piles up. :)
I was implementing separate BT filters but went back to just rate limiting the data going to the BT LE module over UART to avoid buffer overruns on the module. Try setting the filter using 0x03 just like you would over USB Serial.
Also checkout the new 0.4.5 firmware that was merged in yesterday. You'll have to flash it with arduino, I haven't build a binary yet. It has improvements for the BT LE UART.
Also something to keep in mind is the MCU will send packets out on the last used interface only. So if you sent a command on USB Serial it will only dump back to USB Serial, same goes for BT.
Let me know if that helps and how far you get, I'll be checking the forum more regularly now. I've been trying to find time to build the Android Wear BT CBT app. That should be a fun one!