Michelle, just be careful on whatever link building techniques you are using. Don't overdo any one kind of links. Think natural. Also, I'd recommend building more brand links to build your overall domain authority rather then getting the perfect SEO anchor text links. Think long term. You don't want your website to get penalized for manipulation of the SERPS via Anchor text link building.
As for your question about links to your main domain (homepage) or deep links, I'd say go for a combination without trying to do too much anchor text links. Concentrate on trying to build great content that people naturally link to and share. That would do the perfect link building for you.
I hope this helps.