When I click a tracking icon it flashes briefly and still stays at “not tracking”. What is the probable cause?
One of the RA limits that have been set in EQMOD has probably been reached.
The ability to track past the meridian depends on the telescope and where it is pointed. A short telescope can track quite a way past the meridian before it runs into the mount. A long telescope can't track as far. A telescope pointed near the celestial equator can track farther past the meridian than a telescope pointed near the zenith. The Orion Atlas doesn't have safety stops built in. The EQASCOM driver lets you set safety limits.
When the Auto Meridian Flip is checked, does it work if the overall Limits setting is not checked?
Answer: It is the RA limits (meridian limits) that define the point at which the mount will perform an automatic flip. If limits are off then the RA limits are not applied and so there will be no automatic flip whilst tracking and automatic flips will only occur during gotos.
It is entirely up to you how you wish to guide. One option is to have PHD send ASCOM pulse guide commands to EQASCOM which in turn will apply the necessary corrections using the serial link. EQASCOM has a number of parameters that control how pulseguiding is applied and includes a pulseguide monitor display to help diagnose and correct problems.
Alternatively you can have PHD control the mount via ST4 (assuming you have a guide camera with an ST-4 output or a GPUSB/relay box) in which case EQASCOM plays no active part other than providing a means to set the mounts ST-4 guide rate.
Please note that if using the very latest version of EQASCOM (V1.25c) you need to select your preferred guiding method form the EQASCOM setup screen (EQASCOM will then customise the runtime user interface accordingly).