The first question I have is regarding Melee Bite attack. It reads as:
"Bite +4 (1d3-4)"
I think I know what the 1d3-4 means, but I have no idea about the +4 and it would probably be better if someone just explained the whole thing.
Roll a d20, then add 4. That's your attack roll. If it meets or exceeds the target AC value, you hit.
If you hit, roll a d3, then remove 4 from that value. In most cases, this will result in a negative value, so you do instead one point of non-lethal damage. Given spells or equipment, this may eventually become a positive number, which will do normal lethal damage.
I highly recommend not using your familiar in combat. This makes him a target, and if it dies, that sucks. Also, if the familiar is smaller than Small size (Tiny, Diminutive, or Fine) he does not threaten 5' away, and must move into the square of an opponent to attack, which provokes an attack of opportunity.
The other question I have is regarding his skills. He gets a +6 to both Fly and Perception. What exactly is this plus 6? Is that the actual skill check modifier, or is it the ranks or something?
Is it a racial bonus? If so, you just add it to his total skill value. Lets say Fly is a class skill, his dex is 12, and he has 1 rank. His Fly skill will be at +11 (1 rank, +1 dex, +3 class skill, +6 racial). In order to make a Fly check, roll a d20 then add 11.
For ranks, you use either the normal ranks for an animal of that type, or your ranks, whichever is higher. Always use the Familiars ability modifier. If your dex is 20, and his is 12, he still uses the 12.
Under statistics it just says "Skills: Fly +6, Perception +6."
That's his normal total skill bonus, then. Roll a d20, then add 6.
Also, where would I find out what ranks it would normally have?
It's kind of awkward and you work back from what it says in the statblock.
To break it down, he's a 1-HD creature, so he can only have 1 rank.
He gets a +4 bonus to Fly for being Tiny. (See: Fly Skill)
He gets a +2 bonus for having 15 Dex.
So he has 0 ranks in fly.
His Perception is listed as +6. If his rank is in Perception that would add up as: 1 rank, +3 Class skill, +2 Wis = +6, which matches.
At level 2, if you have 2 ranks in Fly, then you would use that instead of the 1 rank a normal raven has. So it would be 2 ranks, +3 class skill, +2 dex, +4 Tiny = +11. (Assuming you are able to take ranks in Fly)
If you have 2 ranks in Perception, his perception score would be +7: 2 ranks, +3 class skill, +2 wis.
Remember to check the section for Familiars under the Wizard class (even though you get the familiar through the Witch class, it uses those rules).
That means, for instance, that the familiar uses its master's BAB instead of its own, and that the familiar may use the master's skill ranks instead of its own, plus a host of other special rules and additional abilities.
Interestingly, the PRD version of the Raven doesn't have Skill Focus (perception), while the Bestiary version does. (The PRD, on Familiars)