They're both Corsair Vengeance same timing C9 etc... just RAM size is bigger and was wondering will I come across any issues? or should I just buy another 2x4GB?
It might and it might not. The only way to know for sure is to put it all on the motherboard and turn it on. If it locks up, during or after the boot process, you have your answer. I would stress test it overnight if it does get to the desktop. And just keep the thought in the back of your mind that if really, really weird things start happening, crashes, lockups, random shutdowns, it could be the memory.
2) You won't be able to have it setup automatically (i.e. XMP) because that relies on a single kit reporting what it is.
3) Since you have a Z97 board, you probably have a feature that will attempt to overclock the CPU (which changes memory as well). You can try that as one option.
If the memory frequency and timings appear to be in the ballpark leave it alone for now. If not then set manually:
4) To set MANUALLY:
Set frequency CAS etc manually. I don't have same board so can't walk you through step by step.
Other:
I manually installed TWO different kits (with different specs) in a computer a few years ago. It crashed. I then manually changed the settings for frequency and timings and got it stable under MEMTEST
Like I said, try it. We can talk about this for years. But the only way to know for sure is to put the memory on the motherboard and turn the power on.