Which wire is line vs load wires
Those colors

OK, so B2-B5 (blacks I assume?) are hot all the time, and would be even if B1 and B6 were disconnected.  Those four wires perform the following 4 jobs (and I really don't care which is which, as it's irrelevant): 


Always-hot from the supply
Always-hot onward to other points of use
Always-hot to switch 1
Always-hot to switch 2


I like to force particular color codes

Now, cables are made in particular colors, but that does not reflect what functions those wires actually do. I like to re-mark wires using colored tape, using the following color code: : 


Bare, green, yellow-green: Ground (mandatory per international law)
White or gray - neutrals (mandatory per NEC) 
Black - always-hot (unswitched) 
Red - switched-hot e.g. to a lamp
Blue - alternate switched-hot
Yellow - 2nd alternate switched-hot
2 yellows together = 3-way travelers
2 blues together = alternate 3-way travelers
2 reds together = 2nd alternate 3-way travelers


B2-B5 are always-hot and are already black.  I would recolor B1 to red... and B6 to blue.  And also recolor the wires that they splice to from the wall.  So now that your wires are identified, they are same color to same color. 

The colors of wire nuts

Colors of wire nuts are a different deal.  They designate wire nut size.  Red is "the biggest in ordinary use". Yellow is next down, fit for 2-3 and sometimes 4 #14 wires.  Orange is good for 2 wires.  They have a lot of overlap in their ranges, but for instance four wires would be too much for an orange. 

Their ranges are published and it's best to stay near the middle of the nut's working range.  You can stretch a yellow to work where a red is ideal, but better to just use a red.