you can go to www.confetticakes.com and Elissa has several shoebox and shoe cakes in her gallerie.
As you will notice, she cut out the box and the top cover the same size, only the cover is about 1" wide and the box about 4".
The way I would do it, and bear with me because I have never done it.
1 - Measure out a real shoebox just to have an idea of the porportions of the box and then maybe add a 1/2 - 1" to each measurement. Layer, fill and coatcrumb, then cover w/fondant.
2 - For the tissue paper, this I figured out the same day i made my own...Just roll out very thin gumpaste, cut into squares and then lift it from the center like you would real tissue paper for giftbags. Fill the gaps with cotton paper so that it retains it's shape once dried. (Notice how it's shaped in her picture)
3 - For the top, do the same as with the bottom, just making sure you've covered the board entirely with the fondant. It may be good to use foamcore, which is a laminated lightweight foamboard you can get at any art store or craft shop. Once done, you may want to cut a dowel that extends about 2" above the cake in the center so that serves as support to the top cover one you fix it on top of the cake, and then fill with your tissue paper.
Although, now thinking, it may be better to set up your tissue paper on top of the box...that way you now how much you need to make and how much you need to fill in each crevice to achieve the fullness you desire.
It's a learn as you go process...That's how I figure out my how to's...Just look at the cake I want to try out and contemplate possibilities and how you would accomplish things using other mediums instead of sugar.
Hope this is somewhat helpful to you...I may try it out someday 
For the shoe, that would be with pastillage, which I have never worked, but I'm sure you can get a recipe on line. Improvise...That's my recommendation....You can do it! 
Godiva
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