Mixing weapon and natural attacks is a mess. Fortunately, it is not what happens in this example.
Here you see 2 full attack options: one for 4-hand multiweapon fighting (iterative attacks from main hand, single attacks at highest BAB from off hands, no penalty for multiweapon fighting due to racial ability) and one for all-natural full attack (several natural attacks at highest bonus each). And it looks like this creature has 6 hands, but only wields weapons in 4 of them.
Yes, the spear ignores negative progression because it is used in different hand.
Ever-helpful Pathfinder SRD link, just in case.
A few suggestions. Some of which may require your DM to be fine undoing decisions already made.
I don't know what system you used for picking stats, but I would say for a powerful rogue you have them in the wrong order.
For a general purpose rogue, I would say dex > cha > con > str > int > wis. If you want a more combat focused rogue, drop cha down behind con and str.
Int is not needed to any huge degree (in a 4+ person party), a rogue will already have enough skill points without taking such a high int. You are better off having higher cha and being better at a smaller number of skills. If the party is 2-3 people, then maybe more utility is worth the tradeoff.
The 12 wis (higher than str or con) is unlikely to provide you with too much mileage. The bonuses to spot and listen aren't going to be all that important for you (unless the DM pits you against lots of enemy rogues), and I would say the +5 hp and +1 fort save will keep you in the fight more than the +1 will save.
In a few levels time, you should be getting enough money that you can get a ring of invisibility. This is critical. It will increase your damage (sneak attack more often) and your survivability.
If I were you, I would not worry about improved initiative. Once you have the ring of invisibility, you wont be targeted before you attack people, and you don't really want to attack (and thus become visible) before the other melee characters have got in. Most rogues have the problem that they go first, and don't want to. Instead, I would go for weapon focus, or for iron will (+2 will save) if there are lots of spellcasters around.
I would recommend against taking much of a fighter dip. Unless your enemies are mostly undead. Each level you are taking in fighter is a level that doesn't give sneak attack damage and doesn't give hide/move silently as class skills.
Best Answer
Hit dice have no impact on attacks
Your Hit-Dice have nothing to do with your attacks, and are related to your HP max and HP recovery while resting. They're "hit dice" as in "hit points", not as in "hitting enemies".
Two Weapon Fighting attack sequence (At level 1)
Attack with first dagger (Main action)
Roll 1d20 + 3 (dex mod) + 2 (proficiency)
If this roll is greater than target's Armor Class, you hit. Roll for damage:
1d4 (dagger damage die) + 3 (dex mod)
This amount is subtracted from the enemy's HP, provided they have no special defenses.
Attack with second dagger (Bonus Action)
Roll 1d20 + 3 (dex mod) + 2 (proficiency)
As before, if this beats target AC you hit. Damage changes though:
1d4 (Dagger damage die)
On the second (off-hand, if you will) attack, you do not add your dex mod to the damage.
Other modifiers
As a rogue, you may have access to a Sneak Attack - this can only apply to one of your attacks each turn.
Advantage or Disadvantage will make your d20 attack rolls work differently. For Advantage and Disadvantage you will roll twice and use the better or worse roll, respectively.