I use Squadron white putty without any problems, though that's not to say that I'm closed to trying other products-I'm tracking down the 3M Acryl blue, and I have tried 2-part automotive putty, too.
But Squadron works with relatively little effort for me. I apply it to a seam with a flat toothpick, or with a dental spatula (which dental staff use to apply their putties to a tooth's surface). Then I take a cotton swab dipped in acetone and wipe it across the puttied area, to remove the excess and to help make sure the seam has the putty in it. That cuts down on the sanding.
I will also take a dab of the putty and put it in a well in my palette, then use an eyedropper to add drops of acetone and make a thicker version of Mr Surfacer, and apply that to the seam with a brush. I haven't had any problem with either method.
The 2-part auto putty was a bit of a problem, because I didn't mix the putty and catalyst in the right proportions, so it didn't cure properly (the instructions are based on using the whole can; I was working with a thimbleful).
A very good tip was mentioned above, and that is to plan your build in such a way as to avoid causing bad seams, or to minimize them. That goes hand-in-hand with reading the instructions carefully and examining the kit, to see if you can spot potential problems.
For example, in an aircraft kit with a 1-piece lower wing half, and upper wing halves, the instructions usually direct us to glue the upper halves to the lower wing piece, then glue the whole wing assembly to the fuselage. But that often leads to seams along the upper surface join at the wing roots.
A way to avoid that seam is to attach the upper wing halves to the fuselage, then glue the lower wing to the fuselage and upper wings. If anything, you might have seam work to fix, but on the underside, where it's generally less noticeable. I used that technique on the Eduard 1/48 P-39Q, it worked really well.