I have a 98 Toyota avalon with a stock 4 speaker setup on the doors with a stock deck

I am slowly going to begin to change the stock system and upgrade to something alot better

My plan is to first buy a new deck and 4 new speakers, I am really new to this so I would like to ask for some help (By the way, the speakers are 4 inch)

What is the difference between 2 way and 3 way speakers, and what is the best way to set up the speakers to get the most out of them, and also when buying speakers can you only buy them in singles, for example 1 speaker for $150)

After this I am planning on putting in 2 subwoofers and an amp

 

speakers usually come in pairs.
subs are usually one at a time.

2 way is usually a midbass driver and a tweeter. coaxil is they both fire from the same spot where component kits car be seperated and placed for better staging.
a 3 way is either a midbass, with another smaller mid and a tweeter.
a good 3 way system is usually worth upwards of 300-400 bucks..(thats very general because i know about prices lol)