PCB123 does not support blind or burried vias. All holes that you place on a PCB123 design go all the way through the board. I have had a handlfull of customers design boards in sections then purchase the gerber and drill data for each layout. You can then combine the gerber output into a single multilayer design. You would then have to manually edit the drill tool sizes so they are unique in for each section of the boards. You don't want a tool size 1 in each drill file.
You may need to go with a different tool for a board with blind/burried vias. Eagle supports this type of vias. Remember that if you submit a board with blind/burried vias you will need to submit your design through the Custom Quote service at http://www.sunstone.com