First things first--
Buy the Lyman's Casting Bullets book and read it three times. When dealing with 700 - 900 degree F molten metal, you don't get many second chances when it comes to safety. Best to know exactly what you're dealing with before you start.
I melt my source lead in a cheap dutch oven I got from Academy Sports for ten bucks. I skim off the clips and trash with a slotted steel spoon I got at the same place for five bucks, and pour the cleaned up lead into the ingot moulds using a shallow ladle steel spoon I also got at Academy.
For flux, I use small chunks of candle after I've skimmed all the trash and clips off the top, then I shave some Ivory Soap (for the stearic acid--a great cleaner) into the mix, and then stir using a pine stick or paint stirring paddle.
Be aware that when you put the candle wax in, you will get a "poof" and a flame--which is good. Let it burn itself out, then add the Ivory soap and stir. Stir, stir, and stir some more--especially going around the sides and across the bottom. Don't "whip" the lead, but stir slowly and evenly. This will bring all the impurities to the top for you to skim off.
For the final skimming, I use a stainless steel putty knife that's about an inch or so in width. It allows me to get every last bit of dirt and slag off the top of the molten lead. The result is I pour VERY clean lead into my ingot moulds, and this helps keep my casting furnace much cleaner. When casting boolits, I have to flux very little--usually only using a pea-sized bit of paraffin or beeswax and some more Ivory soap shavings.
Like some others, I use dedicated ingot moulds. I use the Lyman moulds for my wheel weight ingots, the Lee one-pound moulds for pure lead (plumbers lead, roof sheeting, etc) and the Lee 1/2-pound moulds for linotype ingots.
Some folks use custom made moulds and label their ingots with a magic-marker--works just as well. Just make sure you know which alloy is which after you've poured it into your ingot moulds.
There is no better place on the world wide web than castboolits.com for learning the magic, art and science of casting boolits. That's the place to start above all else.
Jeff