It is easy to get confused with all the equipment choices, especially when starting out. :)
I was going to buy a package of bees with a queen, but the apiary who gave me the hives, is selling me a nuc
What size frame do you have? (Probably either 'Deep' or 'Medium') Are the nuc frames the same size? How many frames in the nuc?
At this time, I have an 8 frame bottom box which was set up for me...it contains some frames that have new wax foundation a couple that look to have wax built up on it by former bees, and one that actually has honey and wax build up on it
Hopefully frames you already have and the frames you will be getting with your nuc are the same size. If so you will want to set aside your empty frames and replace them with the frames from your nuc. It would be easiest to simply put the nuc frames in the middle of your box (in the same order as they come in the nuc) and fill the rest of the box with your drawn frames. Alternately, I would place one of your drawn empty frames between a brood frame and a honey frame. 2 or 3 of the nuc frames will have brood (eggs, larva, and 'sealed' brood with round brown caps the cells.) At least one of the brood frames should have mostly honey. Just remember to keep the brood frames together and place the honey frames around them towards the outside of the box. :)
It seems I should have the stuff at hand?
It is always a good idea to have extra equipment ready. You won't need a second box right away, but eventually you will need several boxes. Give them time to build up so they can keep the additional space warm enough to raise brood. Wait until the bees are covering more than 6 of the 8 frames in you first box before you add another. How long that will take depends on several factors. With some pre drawn frames, and good weather, I would expect to add a second box to an 8-frame deep hive started from a 5 frame nuc in about 2 weeks.
Will the next box level be the storage of honey for the bees??
They will store some honey with the brood, especially towards the top of each frame and towards the outside of the box. However your 'surplus' honey will eventually be stored above the brood chamber. If you are using 'deep' frames I would plan on having 2 or 3 8-frame boxes for the 'brood chamber'. If you are using mediums I would make that 4 or 5 boxes. You will want at least 2 honey supers on top of that.
And can one purchase the frames with the foundation already in place???
You can purchase many different kinds of frames (wood or plastic) and foundation (wax or plastic.) You can buy plastic one-piece frames that do not need to be assembled, or you can buy preassembled wood with foundation if you want, but for some people putting them together is part of the fun. :) There are probably more opinions on what size/kind of frames to use as there are options. Using all the same size equipment has it's advantages, but for what it is worth, I am using deep wood frames (with wax 'starter' strips) for my brood chamber, and medium one-piece plastic (Pierco) frames for my honey supers.