As long as you want to make a bigger batch all at once, the lip balm trays are the way to go! And the source Sheri posted above is great, I have ordered stuff from them occasionally. If you want to stick with smaller batches, I have personally found that pipettes don't work well with thicker balm - and you shouldn't fill the tubes too hot or you can damage the twist up mechanism. I have gotten tiny funnels from Lotioncrafters that work well: http://www.lotioncrafter.com/funnel-34mm.html
Catherine Farmgirl #1370 City Girl By Birth, Suburbanite By Location, Farmgirl at Heart
I have only done small batches. I put the tubes in a plastic container, and pour slowly and carefully. It has worked pretty well, cause anything I spill, I can scrap up and remelt.