My installation is tucked behind the headlight and wrapped in shrink tubing and tape, there's nothing to see back there but a black mass. That's why I suggested the longer leads so that mess can be moved under the tank. I also have a headlight modulator and additional relays that control my auxiliary driving lights as well as accent lighting. These have manual and automatic settings via switches on the bars (I have a two switch Tiumph pod on both sides) so my solution will be quite different than what's suggested.
The Eastern Beaver harness is very easy to install ... the only connections are to the battery and taking place of one factory headlight. Essentially it just plugs in place of one headlight and uses the two headlight plugs on the harness instead. The most difficult part is routing the harness into the buckets and to the battery. If you opted for the switched control, just route those two wires to a location where you want to mount a switch (I used the plastic trim cover on the right side behind the motor).
Eastern Beaver's website has installation instructions but they are pretty much what I just said. Their diagram is different in that the R3 has two (2) H4 sockets rather than one.
The two blue connectors you are talking about are probably the Posi-lock wiring connectors he includes with the kit just in case you want to cut off the H4 plugs and wire it directly. That's optional and saves fishing the H4's through the headlight buckets. If you want to do that, just do one wire at a time so you don't get confused.