I have a large cake to do for this Saturday. It's my first "big cake" ( 5 tieres etc). Would love to get an early start like Wednesday and Thursday but if I cover them with fondant on Wednesday or Thursday they won't still be fresh on Saturday will they? When should I start the covering and how do I store it so it stays fresh? (or do I store it at all....maybe I let it sit out?)

It depends a lot on your cake recipe and things like syrups & fillings etc. Frosting/ganache and a layer of fondant seals up a cake nicely, and fondant is best left to breathe...so I would just leave it out covered loosely with a sheet of baking paper (assuming you have not used a filling or frosting that must be refrigerated.)

What day are you actually baking them?

Cakes baked on Wed, if stored properly, would be fine to serve on Saturday.