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I don't think there is a "best" technique. It will depend on the situation and the image.
Stacking filters? You pretty much need a holder. Just one? Handholding can work okay... unless it's a long exposure and then maybe you don't want to stand there for a minute and hold a filter to the lens.... Maybe the camera's hanging over a cliff and you can't handhold without being in danger of falling over... Maybe you've only got a hard edge, and need to feather the filter for a softer transition, so you handhold... You get the picture.
FWIW I would recommend going straight for the 4x6 size. Here is why:
1) 4x6 filters are easier to handhold without getting your hands/fingers in the frame, so it opens this possibility up
2) the larger coverage is more amenable to wide angle lenses without vignetting (particularly when stacking with multiple filters or a CPL)
3) 4x6 hard edge filters, when moved to one extreme, can serve as a full ND filter too. So one filter does the job of 2, making them more effective in the field, and helping to offset their higher cost with increased usability
4) if you're DX and moving to FX, it's easier to port your 4x6 filters, especially when talking about wide lenses