how to show my categories

This is my first shopping cart to build so I am unsure how to show my categories. Please excuse me if the question sounds easy but I think about it a lot and I make it harder for myself the more I think about it.

I understand to make categories and to put in products but do not know how many level to go. is it normal to go more than one level down from the first category or would it become very confusing to do so?

I keep thinking of a tree as with windows explorer with folders as categories and products as files.

I cannot explain this well because I am not sure I know what to ask.

If I have a product that could be in more than one category must I put it into each category?

for an example I have perhaps an orchid such as "hardy chinese spring flowering bletilla orchids" would I have categories for:

Hardy orchids
Chinese orchids
Spring flowering orchids
Bletilla orchids

I know keywords should take visitors straight to the page but if they are on the site already, what is the best way for displaying the categories?

Another example is perhaps for "designer mens gold dress cufflinks" would I have categories for
designer cufflinks
mens cufflinks
gold cufflinks
dress cufflinks

thank you
Ivanna