Unfortunately there is no way to change the default notes for a blank pattern but you can sort of get around that.
Make a sequence in MCC on one of your sequence tracks with the new defaults you want. Copy that to all the other sequences by dragging and dropping it to each. Save this with a name you will remember is your new defaults. Now drag the entire project from the bottom file browser section on the left (the MCC projects browser) to the to section above it (the BSP projects browser). Now you should have the new "defaults" in your BSP. When you want to reset your projects, hook up to MCC and drag the "defaults" project up to the BSP again.
Now, I haven't tried this myself and thinking about it, making a sequence with all new default note values will give you a sequence that has a string of (say for the example) E4 notes all triggering on every step. To over come this, when you start your BSP outside of MCC, turn all the steps off. The way the BSP works is it remembers he note value assigned to a step when it is turned off so you can mute notes in a sequence on the fly, then bring them back in again without having to reassign the note values. Now you will have a essentially a blank sequence that will activate an E4 note for each step when unmuted.
Hope this works for you.