As the AlphaPix will only let you select 1 pixel chip colour order, you have to decide which it is to be (either the bullets or strips) and select on the controller accordingly.
Then in xLights in the Layout tab change the String Properties / String Type of the incorrect ones to their colour order.
However when in test mode of the AlphaPix or test mode of xLights the incorrect ones will appear (lit up) "incorrect" (you'll have RGB on one type, BRG on the other type; for instance). To check you have the right order you could make a short sequence with say 3 On effects, one of each colour.
One thing to note: in xLights test mode, if you expand the controller you will see each channel listed with the colour being transmitted, so you can also use this to check the correct colour is being transmitted. You will have something like this:
Channel {B} [1] (113)
Channel {R} [2] (114)
Channel {G} [3] (115)
..
..
..
Channel {R} [151] (263)
Channel {G} [152] (264)
Channel {B} [153] (265)