The Fireball description says:
A fireball spell is an explosion of flame that detonates with a low roar and deals 1d6 points of fire damage per caster level (maximum 10d6) to every creature within the area.
Let's say that my caster level is 8. Does that means that if I prepare a Fireball spell it is going to be 5d6 of damage, or do I get to choose the maximum damage it does?
Also, if I prepare my spell as 5d6, does it still fit in a 3rd level spell slot?
Your caster level (CL) is 8. Your maximum spell level is 4th. Fireball is a 3rd-level spell. Spells can be prepared in higher-level slots, although this does nothing special*. You can always cast a spell at a lower CL than normal**, down to the minimum CL needed to cast the spell for your class (in this case, 5th or 6th, depending on whether a Wizard or Sorcerer is casting it — presumably the former, given the mention of preparation). And fireball damage scales only with CL, per the original rules quote.
Therefore, you would cast fireball out of a 3rd-level slot for 8d6 damage normally, or as little as 5d6 damage at your option.
In two more class levels, your CL would be 10 and you would be casting fireball, still out of a 3rd-level slot, for up to 10d6 damage. After that, you don't get any more damage increases from the spell itself, although there are lots of feats and class features and what-not that can increase damage in various ways.
A spellcaster always has the option to fill a higher-level spell slot with a lower-level spell.
You can cast a spell at a lower caster level than normal, but the caster level you choose must be high enough for you to cast the spell in question, and all level-dependent features must be based on the same caster level.
