I am working for two education site... For both for them i am working same but link generating for both the site is different... I dont know what is reason.. Can any one help me.
For link Generation you can submit your site url in do-follow social bookmarking sites, can do blog submission and forum commenting by enabling signature. These are effective ways to generate more links.
If you are doing the same number of submissions for both the sites but one of the sites is not getting in rankings then there might be problems with on-page optimization that has been done for the sites or one of them has duplicate content issues because of which it is not getting good ranking.
Sometimes using same IP's to submit links of two different websites may not work well. Some directory owners tracks your IP's and dont allow multiple submissions just like in DP you are not allowed to have 2 accounts on same IP
I would suggest to add website into good PR directories . It will help straight away . I know some good ones. But thing is , they need to be very SEO, well linked and based on good script. It is quite difficult to get quality backlinks at the moment where everyone offers 2000 submission for 10 usd or something .They are not good . I will consider to submit links manually for others next month to show that after 20 submissions ( approved ) you can get better results than after 2000 submitted ( submitted - not approved - its important to know difference )
i didn't get your point, did you mean that counted backlinks are different for both website ? if yes then it happen because content of each website are different so some links are counted in one some are counted in other