If the template just has one repeat of the pattern on it..so you would need to keep moving it along to get a trailing effect, it would be easier to complete each whole stencil first before moving it along?

Otherwise you would have to do all the yellow, move it along, do another all yellow move it along etc...then you would have to start from the beginning again with the next colour, but you would have to reposition the stencil back on exactly the same spot.

So if your final design is ten stencil lengths you would need to reposition it thirty times, if you do the colours one at a time. But if you completed one whole stencil before moving it along, you would only need to reposition it ten times.

It may be simpler to do all three colours on the stencil and move it along, then do all three colours again. Use three different brushes for the three diff colours, keep the brushes as lightly loaded with paint as possible and sort of scrub gently with the brush where the colours meet, to give a smudgy blended effect. There shouldn't be enough paint on the brushes for the colours to run.

But if it is just one really long trailing stencil then do as Carol said. One colour at a time. Sounds nice.