Answer to Q1:
Yes, provided the spectral accelerations are normalized values, meaning, they are divided by "g". In other words, if the spectral acceleration is 490.25 cm/sec^2, and you specify it as 0.5, then, the scale factor is 980.5
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Answer to Q2:
No if you have provided the spectral accelerations as normalized values.
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First, instead of specifying the direction factor as 1, specify it as I/R where
I = Occupancy Importance Factor
R = Response Modification factor
The source of this information is section 12.9.2 of ASCE 7-05, which is what the IBC 2006 implementation in STAAD is based on.
Then, run the analysis again and compare the base shears.
In ASCE 7-05, section 12.9.4 states that "Where the combined response for the modal base shear (Vt) is less than 85 percent of the calculated base shear (V) using the equivalent lateral force procedure, the forces, but not the drifts, shall be multiplied by 0.85 V/Vt :
where
V = the equivalent lateral force procedure base shear, calculated in accordance with this section and Section 12.8
Vt = the base shear from the required modal combination
Since the multiplication by 0.85 V/Vt is to be done only for the forces and not the displacements, you could create a load combination in which the factor of 0.85 V/Vt is applied to the spectrum case, and use that combination case for steel or concrete design.