I have sections on my site divided into subdomains,but i noticed subdomain wont be credited for main site backlink as directory. Example: domain.com subdomain.domain.com -if i put subdomain.domain.com domain.com wont get backlink credit domain.com/directory -in this case domain.com will be credited as backlink Also,how can some sites have bigger page rank in sections then on homepage?
I prefer subdirectory section because I can interlink those sections as much as I want. IMO excessive intelinking between subdomains could be a negative factor on SEO terms. Simply getting more links and/or links from higher pages to inner pages than to homepage.
Subdomains are just treated as separate domains by the search engines. If you want the interlinked pages to be credited to the same domain, just use a directory structure instead.
subdomains are completely new domains for search engines. if you can do, i suggest you to create a folder for every subdomain on your site and use 301 redirect from subdomain to the folder