Alright basically im curious to know is it worth getting Sorc boots over Merc on heavy CC team also as well as instead of Magic pen runes Magic resist Runes Would Magic Pen really make that big of a difference in damage?

Matters how much the opponents stack MR, but yes, MR can seriously gimp your damage.
Remember there are more magic pen items then sorc boots, and merc boots are still the best for tenacity.
How important magic pen is based on how much magic resist the enemy or your main targets have.

Just like Flat MP Early game not worried about it late game just wanna know if its really worth it early game or not.

It's extremely useful early game for magic based champs.

It's hard to speak entirely generally, as it depends on champs somewhat, but most of the time it's pretty great. That said, if you have more pen than enemies have resist, it's wasted. So it's not always useful to get a ton of it.

And if you plan on getting a Void Staff, the flat stuff isn't as exciting.

Early game only. Late game should have swapped for Merc Treads and grabbed Void Staff or Abyssal Scepter.

Survivability is top priority so Mercs is usually better. You usually only take Sorcs on early game heroes like annie/leblanc or if your opposing team sux really bad

Sorc boots should only be used on heavy bursters like leBlanc and Annie. That being said the best option for magic pen is to get void staff as your 4th or 5th item when every char is starting to beef up. The magic pen runes should get the job done until then.