Kentico's API handles a lot of that, This is all you need to do to properly set a password and let Kentico handle the encrypting:
CMS.Membership.UserInfoProvider.SetPassword("Username", "ThePassword");
What i would recommend is make a new column in your excel, and then use the CONCATENATE function to build the above line. Say column "A" is the code, Column "B" is username, and column "C" is the password. In column A in excel, put:
=CONCATENATE("CMS.Membership.UserInfoProvider.SetPassword(""",B2,""", """,C2,""");")
Then just drag that down all the way, copy and paste and run it. Little trick i use a lot.