Theres actually serveral ways to tackle these 'tricks'.
1. Sinking bolts. I will describe the easiest way to do this. You will need two or three drill bits (two for soft wood, three for hard), the type of bit is irrelevent, any bit will do as long at the size is right. First thing to do is take measurements of your carriage bolt. The first one if the size of the threads (you probobly wont have to measure this one, ax. 3/16 Carriage bolts are obviously 3/16th threads) Another measurement is the head of your Carraige Bolt. Using a set of calipers makes this an easy task as using a tape measurer is bit less accurate but possible. When you determine that size, find a drill bit exactly this size or a little larger. The last measurement you only need to take if your using a hard wood like oak. That measurement is from two opposite points of the square under the head of the bolt. You need a drill bit that is almost but not quite the same size.
Now, you mark the wood and drill your hole that is the same size as the threads, next you use the bit that is larger then your head, and only drill down 1/4 of an inch, enough so that the head of the bolt wont show. Now, if you have soft wood then your done, as when you tighten the bolt down, the square of the carraige bolt will puch into the wood, making a square This can be done with a hammer and a punch or tightening the bolt on there alone. One the other hand, if you have a hard wood, you should drill one more time, using the middle sized bit, again you only need 1/8th to a 1/4 of an inch down. This hole allows your square to fit into that hole without turning since it is/should be slightly undersized.
If that isnt very clear I can provide photographs later. ( i can make a couple examples and photo them, if needed)
#2 This one will be easier to explain, but harder to actually do.
The easiest way is to perform a "plunge cut" using the jigsaw, but if you are a neophyte woodworker, that might not be the best route for you. If you are thinking about this route, or would liek to know more about this route, then
This Page can give a better explination.
Now, you never said whether you wanted/needed rounded corners or not, but if you do, then the easiest way is to use one of the hole saws in each corner where the outermost edge of the hole saw is touching both lines, this will give you the room to simply set your jigsaw or rotozip in there and cut from one hole to the next.
Lastly, and possibly the quickest way, if first cut yourself somewhere to start from (or plunge cut), then follow your line all the way to the corner (use a jig if your not good at straight lines, by jig i mean clamp a peice of wood to the wood you are using, as a guide) go all the way to the corner, then back up about 12 inches, and make an arc to the next line, cut all the way to the corner and then back up and arc to the next line (this will do the whole hole in one cut, but it will leave a peice of wood in each corner) when your done, there will be a triangle in each corner, just line the jigsaw up and cut off each corner and then your done.
Again, if something didnt make sence, then I can do an example for you and take photos, if you need.
Hope this helped someone! :-D