trying to decide which I should enchant my items with but I'm not sure which would be more beneficial. I have bunch of sigil stones taking up space and I have some with fortify magicka 50pts and fortify intelligence 12 pts.

Go for the fortify magicka. Fortify magicka 50 = 50 more magicka; Fortify intelligence 12 = 24 magicka.

It may depend on your character, too. Acadian pointed out the sheer magicka value difference, but it's also true that you can cast Fortify Magicka +100 for very little cost, while Fortify Intelligence +100 (or any level) costs quite a bit more magicka to cast.

Depending on your character, you may want to weigh the difference in casting costs for the two effects, too. It may be better to take Fortify Intelligence as an enchanted effect rather than casting it.

Here's a cool trick you might know. Add this to any spell, and you can almost have an infinite magicka pool until effects run out.

Fortify Intelligence
Self
100 pts
x secs
+
Fortify Magicka
Self
100 pts
x secs
+
Drain Magicka
Self
3 pts (least amount allowed)
x secs

As long as you keep casting the spell within the x secs, you can have an infinite pool of magicka. The magicka cost of the spell cannot pass 300 pts (100% of spell effectiveness) or 285 (with 95% spell effectiveness). Of course, you can lower magnitude of Fortify Intelligence (NOT Fortify Magicka) or remove it if you want a less powerful spell.

Yes, that's spell chaining (without the Drain Magicka and only the Fortifies, that is), and I have posted about it many, many times for people who think they need a lot of magicka or that having lots of magicka even matters at all in TES (it doesn't, of course).

One correction, though: the max spell cost is 150, not 300 (100% efficiency, of course). You cannot exceed 150 or you will not have enough to recast the spell chain... and you'll run out of magicka very quickly.

The "x secs" is normally 3 for a ranged spell, or 2 for a touch/self spell.

However, my point about cost still stands. Fortify Intelligence is much more expensive to cast than Fortify Magicka, and this might make a difference for the OP's choice of what is the best option to use the sigil stones for.

If you add the Drain Magicka effect, you CAN use all 300 pts of magicka--although I don't know if Atronach users can bc of their Stunted Magicka defect. http://www.uesp.net/wiki/User:Wizy/Chain_Spells explains the mathematics.

Taking your advice on duration, I made this spell--adding the necessary Fortify Intelligence, Fortify Magicka, and Drain Magicka spell effects at the beginning of course.
[Paralyze_1 sec]*** + [Drain Health_100 pts_1 sec]*** + [Fire Damage_86 pts_1 sec]*** + [Shock Damage_100 pts_1 sec]*** + [Light_50 pts_3 secs]*** + [Invisibility_Self_3 secs] + [Weakness to Magic_100%_3 secs]***

***Indicates on Target and a minimum Area of 10.

I added an Invisibility spell, so the player avoids damage if the Paralyze effect is resisted. I know it may seem strange, but I also included a Light spell to indicate when the Weakness to Magic effect wears off. Even if Weakness to Magic doesn't increase Fire and Shock Damage of subsequent attacks (as some may argue), it WILL increase the Drain Health effect of subsequent attacks.

Is it too overpowered and dangerous if reflected? Yes. Is it fun--especially when the controller violently shakes and a group of marauders fly into the air? Absolutely!

Well, the main point is that there is no need for a spell over 150, so adding Drain Magicka is somewhat beside the point. You can do it, but there's little reason to do so.

Also, it adds to the cost of the spell, so the spell effects you want will be lower. This is particularly important at lower levels when you are not casting max power spells yet.

To each their own, though.

I'm happy to see that someone else understands how to create a pure mage type of character, at least. There are so many people who focus only on acquiring a large magicka pool, but that isn't how mages work in TES, of course.

I prefer fortify intelligence, hate that strong purple light surrounding my character. Plus in my mind the difference is too small for me to bother with