It sounds like you need to look at your execution plans and review your execution plans. You may need to add some indexes to the database.
Fire up SQL Profiler and filter based on the DiskIO value greater then 1000. If that gives you to much data increase the number. Then run these commands manually and review the execution plan. Anything which is doing a table scan, index scan or clustered index scan needs to have the indexes reviewed and possible additional indexes created.
If you are seeing only seeking it may simply mean that your database load has outgrown the capacity of your disk array.