Ah, but you must keep in mind toems and manuals give inherent bonuses. The stat bonuses from the prestige class are also inherent bonuses. They don't stack.
So if used a manual to get a +2 Strength, and then added 3 points to Strength from the prestige class, you'd still only have a +3 bonus.
(It's like using a Wish. Using five wishes in immediate succession gives you a single inherent bonus of +5. But if you use one wish per day for a week, you'll just get the same +1 bonus multiple times; if they're applied to the same stat, you'll have wasted a lot of XP for only one stat point.)