New iphone4 question

I just upgraded to iphone4 from 3gs, I have been reading some of forums postings advising that benefit from iph4 battery life I should not restore from 3gs. My problem is when I activate as new and bring all of my apps over to new phone I lose all of my critical paswords,acct# ect that I have stored in my fliq notes as well as auto maintenance data I have for all of my vehicles. So I know all of the info from our phones are stored in our itunes, but what I dont know is how to port over particular app data from 3gs to iphone4 and still keep as new