Cloning my SSD into bigger one
Finally solved it.

After countless tries, here is what worked for me : 

Format your new disk using macsx extended (journaled) and with GUID boot table.

Clone your disk into the other disk (in my case SSD to SSD) using Carbon Copy Cloner.
Then go on AppleLogo->System Preferences->Startup Disk and select the disk that you cloned INTO (destination).

Press restart, and it will appear in the booting options.

In my case, after it shows in the boot options I can select it and boot from it (even tho it is still external).

Hackintosh only:
In my case this wasnt the final step, since, after removing the original disk and mounting the new disk it still wouldnt boot.

So, I plugged the OLD disk into the USB external case, so the boot options would show, booted from the NEW disk as in previous step (settings->startup), and then Ejected the OLD disk once it booted, to prevent problems, I noticied that all apps were running normal (important to make sure you boot from the correct disk, since they are clones, you wouldnt notice a difference), and then reinstalled my Multibeast settings.

Removed the old disk from the usb slot before I restarted again. 

Success, now, the new disk is cloned from the old disk, and has boot info re-installed onto it.

PS: if you are also planning to upgrade your OS, keep the old disk around and intact, so you have a quick and complete backup to work with just in case. 

PS2: I use TimeMachine, but I unplugged it before any work just in case I needed it later, suggest you do the same.