HI Raman,
If you paint the car without sanding the car completely and with these putty patches, the paint will be uneven. As you are not expert in painting, so you will be unable to paint the patched surface. If you paint the car in this condition, the putty patch and body color surface will be different in color shade. Putty area will become dark after drying.
In my opinion, you should re-sand the body to bare metal and then fill the putty again to the whole car. BTW how much have you spent in putty and other material ??
Stop the putty work and forget about painting for few days and check the following area for rust and remove the rust completely from the floor, dicky area, wheel wells, near the bumpers. Remove the fenders and check the fender and inside area for rust. Also remove the pads(that hold speakers) in the dicky area and check for rust. And see that there are no holes in that area
Your car should be rust free if you want to keep it for long time with you. Check all body metal and if you find anything corroded you will have to replace that metal by tinkering and attaching new metal.
A hard wire brush, flat head screwdriver, old tooth brush and emery paper of 80 and 120 grit will be required to remove the rust completely. Remove all the rust from your car by scrapping the rust using wire brush. Then sand the surface lightly using 80 grit paper. After sanding is done, remove the rust particles and sand the surface with 120 grit paper to smoothen the surface. At last use acid (available in general store) to mix with water and clean the surface. Mix 30% acid to 70% water and wash off the surface and dry it properly.
After you complete the cleaning process anti rust coating is to be done.