I buy from AccessoriesforFragrances.com. They will include at least one pipette (good for decanting from splash bottles) and a small funnel. I find I don't need to use the funnels unless I'm decanting into a tiny glass vial.
To decant into their atomizers, just point the spray nozzle into the opening of the atomizer and spritz slowly. If you spray slowly it sometimes comes out in a stream rather than a mist and less is lost into the air.
If I'm shipping the atomizer or carrying it onto a plane, I like to further seal the threads with a bit of teflon tape such as plumbers use.
Other sellers of bottles include Lotioncrafters and Pilotvials.