I quit using Atlas switches on my own model railroad when I was a teenager almost forty years ago, in favor of Peco switches. Not long after wards I started had laying track and building my own switches. Now on my own railroad I only use commercial switches on hidden trackage and up on the forth and fifth levels, where hand laying track is problematic due to the proximity to the ceiling. At my local Club (Clarksville Tn- see Bill and Tom's excellent adventure over in the logging section) we have been building mainly with what is on hand. this involves a lot of Atlas turnouts, and I have learned something about minimizing the difficulties with them.
1. use the largest # switch you can, unless you just have tiny equipment, use #6 switches exclusively on the main. in the yard, try not to but #4s directly against each other unless you use small equipment exclusively
2. where the track enters the switch anywhere but the curved diverging track, there should be at least a half locomotive length of straight track, and preferably a whole locomotive length of straight track. This way the locomotive's momentum is aimed straight at the switch. This eats a lot of space up, especially if you have long locomotives and #6 switches; but if you want reliability, that is the price you have to pay.
On the diverging curved track, try to match that curve exactly, or have some straight track. this will help a lot too.
No Vertical curves (changes in the grade) within one locomotive length of the switch. You might get away with very slight grade changes, but anything drastic will cause problems for sure.
these tips apply to any kind of switch, but the atlas switches have some slop in the flange ways, and the pressed metal points are kind of primitive. We can't blame this all on Atlas, when the NMRA standards were written the track standards were written by one committee, and the wheel standards by another. from what I under stand the committees were headed by guys who couldn't stand each other, and they did not consult each other.
When I build a switch, I build it to the track standards, and then tweak it until it works. Commercial switch manufacturers have to make compromises with the standards, and hope they work in the field. At out club, I have used some Atlas switches, in accordance with the above guidelines without much problem.
Bill Nelson