I use both a pen and a brush. Pen is good for smaller spaces. Brush is good when I want to flux a large area for some reason. The specific products I use that work for me well (your mileage may vary, also I am not saying these are the best prices, I actually get the pens from a local Fry's and save on shipping) are:
http://www.ebay.com/itm/KESTER-186-ROSIN-NO-CLEAN-FLUX-FOR-XBOX-360-REFLOW-/131124985951
Time to refill the applicator bottle. I just recently finished off the first full bottle of flux after more than a year. I bought three in the beginning, but I have been using it pretty slowly.