So Im looking at playing a Thousand Sons and looking over the starting skills, Im wondering if they count towards my Alignment? If not, where does my alignment start?

Also the stat bonuses, do they take the place of stat advancements?

ie doe +5 WP mean I have to take WP Intermediate for my next advancement or are the bonuses exclusive?

What about racial bonuses?

" Im wondering if they count towards my Alignment?"

"if not, where does my alignment start?"

​Nope but as the character aligned to Tzeench that means he has at least 5 point worth of alignment towards the Great Deceiver.

"Also the stat bonuses, do they take the place of stat advancements?"

"ie does +5 WP mean I have to take WP Intermediate for my next advancement or are the bonuses exclusive?"

No it is a bonus from the archetype

"What about racial bonuses?"

As far as I know there aren't any racial bonus but character package's from the race you chose.

So what the question here?

To concur with above. The consensus of the forums is that your starting alignment is 5-0-0-0. That also means you only need 15 purchases with your exp to get your mark (helpful since the archetypes tend to gobble up low cost purchases)

It is technically a house rule, but it's worth noting that it's a really sensible, sane house rule.