Hello. 3DPrinterOS Cloud Slicer don't support changing extruder for this moment. But dual extrusion is currently in active developing.
For this moment to change extruder for Makerbot printers you can try to use our new slicer application "Slicer for Makerbots". There is no extruder selecting on Simple or Advanced tabs, but you can change them in Expert tab. When you selected printer type and some of default slicing profiles, you can go to Expert tab and change next parameters:
"defaultExtruder": 0, (extruder number for your model: right=0, left=1)
"defaultRaftMaterial": 0, (extruder number for raft)
"defaultSupportMaterial": 0 (extruder number for supports)
If you leave this settings as is - only right extruder will be used. Changing all of that parameters to 1 - only left extruder will be used. Changing only some of them then both extruders will be used in printing.
Changing of this parameters will properly work only for Makerbot printers with dual extruders: Makerbot Replicator 2X and MakerBot The Replicator (Dual). In any case please make some small testing before printing something big and cool)
We can add default slicing profiles to "Slicer for Makerbots" application with only left extruder selected too, if it will be useful for anyone.
Please let us know if this information is helpful for you. Happy Printing)