Wiring really isn't all that difficult.
First you need to think about where you're going to locate loose items. Route the wires and make sure you get the best "permanent" locations for things. You don't want to be re-arranging wiring after you've done a good job of putting on new connectors. Zip ties are a life-saver here if here are no tabs. Make sure the components are well out of the way of luggage, tool kit, etc. under the seat cover.
Get a simple 12v test light. I bought one of these from Ebay recently and it's a good one - better than most. Bad thing is you have to wait for it to arrive from China, but this is a tool any DIY person should have in his box.
You connect one end to the frame, or something negative earth and poke a wire with the sharp end to check for live (Or better still - at the electrical terminal if there's access). If it comes on when you pull your brake lever, you've found the wire for your brake light +ve.
If it stays on, it's your tail lights (Check the switches and see what happens). If it flashes it's a winker.
If nothing makes it live, then it may be 've earth...
Couldn't be more simple to test electrical circuits with one of these. A multimeter is more cumbersome to use for checking simple continuity. Where you think you may have a broken wire, poke the tester along it's length. If there is a break in the wire, it'll work on one section and not the other. Then you've found your fault.
Get some proper crimping pliers for brass / aluminium terminals / spade connectors (male & female) (Go to a good electrical or car parts shop, they should sell these - Halfords is not the place!) or buy from Ebay if you're a lazy shopper like me.
Get yourself some box connectors too. Say if you have 3 wires going to the brake lights, get a 3-way connector box. 2 way terminals for indicators.
Here's a few quickly searched examples of what I'm on about - available from Ebay.
You can also get a soldering iron and solder. Basically where you want to join two wires you'll be twisting wires together in a continuous line - and applying heat (A larger soldering iron is better than an underpowered one!) to the wire - and the solder will melt if in contact with the joint at the same time. It also helps to "tin" the end of the soldering iron. Check on Youtube how to solder. It's easy-peasy.
Whilst you're buying a soldering iron - buy some shrink wrap, which is a thin plastic tube that will shrink when you pass a lighter or soldering iron underneath to heat it up (Don't burn through it though).
There should never be wires wrapped around one another and held together by insulating tape. That's asking for trouble...
Do the job methodically and tidily. Take your time and THINK / Double check you have everything right (Shrink fit over the wires first & through the box before crimping or soldering!). You might want to practice with the crimping tool first, to make sure you know how to crimp copper / aluminium terminals. If you make a mistake, have spares terminal boxes just in case. These types of connectors are not expensive things to buy.
Hopefully the above will help you get your wiring sorted under there. It's not good to have brake lights on permanently!
Euro RC51 SP2: HRC WSB Ti Hi-Level, T1 Airbox & Snorkel, PCIII, Dymag CA5 Carbon Wheels, Ti64 Spindles (F, R & Swing Arm), Mori Link, Maxton GP7 Shock & Ohlins 832 Forks, Brembo GP Calipers & SBK narrow track (F), Braketech Disc (R), Brembo billet Underslung x 2 Brembo RCS, Tyga Triple, 7075 Stem, Probolt Titanium all over, Babyface rearsets, MR Complete Carbon Lineup, Custom Undertail & CBR 1000 LED, Watsen LED Indicators, Harris Brace, Giles clip-ons, Corbin seat, etc. 2013 BOTY.