Cut off the rear section like this

Slip in the supplied frame plugs. Make sure to drill some 3/8 inch holes around the pipes so you can plug weld these plugs in. This will help to strengthen the union between the pipes and also will keep the plug from falling down into the frame when you install them Since these are sold plugs its not a bad idea to drill into the slug itself also to help get better penetration.

Leave some space between the pipes to make sure you have a nice weld and drill out those pipes to plug weld them for strength

When figuring out where you the shocks will be mounted make sure to keep in mind travel of suspension, how you will set up your rear fender(mounted to the frame or the swingarm)and clearance of the seat to the fender.

Make sure to have the shocks on hand that you will be using to line everything up correctly.  Bolt the shock to the swingarm, move the shock toward the pipes you just tacked welded together. This will show you exactly where to attach the tabs.  Take a tab, put it on the outside of the shock put a bolt thru the tab and the shock and put another tab on the other side and then a nut. Basiclly bolt the tabs to the shock. Line it up the pipes and tack it in place. Do the same on the other side and you should be lined up perfectly. Get it all lined up and weld it. 
Note the larger shocks shown in the pic will require more fab work on your part. You will have to cut the tabs off on the swingarm and make them wider to accomodate. I would suggest instead using a nice progressive shock. Many available will fit perfectly in the stock swingarm location and will ride beautiful. If you are super tight on budget theres always Honda rebel shocks. They will fit in the stock brackets but definately dont ride as nice as some progressive shocks will.
Both finished bikes are built using the brat kit
Installed kit
Leave some space between the pipes to make sure you have a nice weld and drill out those pipes to plug weld them for strength

Depending on which way you slide the plugs in to the new upper tubes it will be a tight fit and may not meet the pipe all the way. This is to allow space between the pipes, especially if you are mig welding the two parts together. Leave a small gap between the pipes. This will allow you to weld the pipes and the plug together all at once.  The main concern is only to make sure you get good penetration on your weld to the plug. Dont over do it. To much is as bad as not enough weld.