Questions as follow:
1) I want to make a design in Illustrator for a box packaging, say of 5 x 5 x 10. How should I prepare the layout? I mean make it like here:
and then just make guide lines!
2) Also, how should I prepare the design for hot stamping process?
This is going to depend on your printer, so you should seek advice from them regarding cut-guide set up. What you or I always, maybe, or never normally do might have little bearing on how they want it submitted.
If I were to do this naively, I see that hot-stamping is a hot-die process which means that the printer will need to have dies made. Therefore, anything which is going to be foil is going to need to be isolated for the purposes of making the die. I would make a separate "spot" color labeled "FOIL." The actual color doesn't matter, just always use it as 100% tint, no fades, drop shadows etc.
As far as the printing of the shape, the actual item being printed will probably be a flat sheet, so just ensure your colors bleed (extend further) beyond the cut lines by at least .125" in case the actual cuts don't align properly. You don't want the actual lines of the folds and cut to be visible in your artwork.
I would probably make a document with layers: 1 with the cuts and folds indicated (folds with dotted rule, cuts solid) that is marked "does not print", 1 layer with only "FOIL", and 1 layer with everything else.
Additionally, I would provide 3 documents each with only one of those layers, clearly labeled. These would basically be copies of the original document where I removed all but one layer. This way, they can send out the FOIL to the die-makers, refer to the CUTS document to setup the cuts without any confusion about content.
I would provide a clear description in writing about what the 4 documents are and why you provided each of them.
When submitting the items I would call or preferably meet with the printing representative and speak directly about the submission items and ensure they understand my intention and that if they find themselves making judgements out of a lack of clarity, they should contact me rather than going ahead.