This is done with the Gerber export in the CAM Processor. You will create named sections and you can have multiple layers selected for that section.
It would probably be helpful to look at some folks cam scripts. The on for DorkBotPDX is a good example:
http://dorkbotpdx.org/wiki/pcb_order The script is in the "How to submit your order" section, but I'll link here as well:
http://content.laen.org/pcb/LaenPCBOrder.camWith your board loaded, do File -> CAM Processor.
You should have the CAM Processor Window now. Do File -> Open -> Job... And select wherever you saved the .cam from Laen.
Now you will have many sections. Notice how Silk Screen CMP will have Dimension, tPlace, tNames selected. If you want more, just select it. Once you get the Job how you like it, save it so you have it next export. The same goes for all layers and you can add some for whatever.
I don't believe there is any risk having silk screen over pads or vias. All board fabs I've seen will only print silk screen on the areas that are also solder masked.