Can payments sent from ServiceM8 to MYOB be automatically sent to undeposited funds?

Yes it can, what you need to do is adjust the banking setting inside MYOB.

So if you open MYOB:
1. Click the setup menu
2. Click the preferences item
3. Click the banking tab
4. Make sure that “When I receive money. I prefer to group it with other deposited funds.” is ticked.

That should be it - any future payments raised in MYOB from ServiceM8 will arrive in undeposited funds.