I'm new to the forums first of all. Glad to be part of a well established community.

This thread is specific to the speakers.
Ok long story. I'm getting ready to graduate from nursing school in a few months and plan on doing an entire new home theater system. I want one in the living room and one up stairs. I plan on using my current system upstairs. The new system will be downstairs. I wanted opinions on speakers. Right now, well its more than I want to spend, but not entirely out of the question as this and handguns (1911's) are my hobbies.
Current System
TV -Samsung LNS4051DX -40" or maybe "42?
Blu Ray Player - Sony BDPS350
Reciever - Onkyo TXSR503
Floor Speaker -Infinity Primus 250
Center -Infinity Primus C25
Bookshelf (rears) - Primus 150
Sub - Infinity PS8
New System
Onkyo Blu Ray Player DVB-D606 -$430
Onkyo Reciever - TX-SR806B -$700
Samsung LN52A860 -$3000
Definitive
Center-MYTHOSTHRE -$550
Bookshelf-MYTHOSTWO-$1100
Subwoofer-IISUPERCUBE -$900
Floor -MYTHOSFOUR -$1400
or I may sub the floors with the MYTHOSTWO and for the rears use MYTHOSSIX. Please give me your opinions. This will be in an average sized living room. We may move, so it's hard to give a definite answer. What I don't want to do is get too much floor speaker and spend more than necessary. Possibly use the MYTHOSGEMXL ($600 pair), one in each corner (2 sets total).
I'm happy withe everything but the speakers. My current speaker system sounds good, but i've never had another speaker system so i'm not sure what else I should go with. Whether I should go with large floor,bookshelf, center speakers or a 5.1 system. I'm hoping someone here is a real audio nut. I'm big on clarity not booming. I do watch a ton of movies and the music I listen to is blues and classic rock (ZZ Top, Led Zeppelin, ACDC, Ozzy). Also should I be running my HDMI from the player to the reciever then to the tv or just from the player to the tv. I'm really new to the blu ray thing. I'm also unsure about running audio through HDMI or through an fiber optic cable. I had also given thought to running four bookshelfs and cutting out the floor speakers entirely. I'm unsure and need help. I just wasn't sure how big of a difference I would get out of any of the new systems since I am watching movies and not really listening to much music on them.