Durga,

1. I have replied for ZPA (Reg. Guide 1.60/UBC -- g's)as given in control parameter. This factor is used for predefined response spectra.As per Caesar help
When used with certain pre-defined normalized response spectra, it is used as the acceleration factor (in g's) by which the spectrum is scaled.Both the Reg Guide 1.60 and the UBC curves are normalized to represent a ground acceleration (ZPA) of lg; the true value is actually site dependent. Therefore, entering ZPA value here appropriately scales any Regulatory Guide 1.60 or the Uniform Building Code response spectra.

However if you want to consider any scale factor for your response spectra , you can consider it as a factor in spectrum load case tab of caesar II.

2. The ZPA value in your second option is related to missing mass components ( response related to non extracted modes). You can find its detailed explanation in the caesar help (c2TR) technical discussion.In my opinion if the acceleration value for both extracted and spectrum option are different in your inputed response spectrum then the result should not be same. Please note to compare the effect of included mass correction you need to chekc the stresses /forces , however the displacement values may be not much affected by non extracted modes (higher modes) because it gets from lower order modes.

I hope i have provided you some idea about your questions , however the best response can be get from earthquake analysis expert.