1.

first i would like to know while in load case for Seismic Spectrum, whether self weight for y is only
enough, or for all directions it should be applied. Also the maximum force as applied on the nodes shall
be only apply for one direction, say X together with response spectrum , or also it has to be again apply
for defining response spectrum for z direction also. 

Ans: In STAAD Pro, we do not have an option of defining mass elements which are nedded for the
Spectrum analysis. 
 So what we generally do is , first apply the Dl + 0.5 LL on the structure, Secondly apply pinned supports
to all the nodes, analyse and get the vertical force in each node and apply the force in all the three
directions for the corresponding node in the response spectrum load case. 
  
If your DL case doesnt have selfweight in it, You will have to apply it along with the above mentioned
forces in all the three directions, i.e ) selfweight y 1, selfweight x 1, selfweight z 1. 
  
If your DL case already has selfweight in it, you dont need to seperately specify selfweight command in
the spectrum load case. I hope i am clear. The reason for applying all forces in all the three directions is
because the mass calculated at the node(done internally in STAAD) must be applied in all three
directions in order to provide inertial forces. 

2. Also i would like to know, whether designing command can be followed after the analysis has been
done in the same staad file, or a separate file has to be created where these interpreted forces should
be applied as an axial force for each nodes for carrying out the design of the frame

As for your second query, it is possible to give the design command after the response spectrum analysis
in STAAD. But i would not recommend it. Because in case of spectrum analysis, the forces of all
the modes are summed up using the SRSS (sum of square root of squares) method. and because of this
the signs of the bending moments would be lost i.e) if you see the Bending moment values for the
spectrum case, all the values would be positive. 
  
This may lead to over design of some sections and unfortunately under design of some sections. What i
would recommend is find the Vb (Base shear ) values of dominant modes(modes in which considerable
amount of masses participate), sum it up and then distribute it to each node using the formula in
equivalent static method. Then apply the forces(nodal forces - static)  in each direction as a seperate
load case and analyse and obtain the results. 
  
The forces obtained in the above mentioned method can be used for the design.