Versions 0.0.5 and above of EQMac provide pulse guiding integration with PHD.
To set this up, you should first run EQMac as normal. Go into Preferences and select Pulse Guiding. This will reveal two configuration options to set the guide rate for the RA and DEC axes. The settings represent a percentage of the current tracking speed. So for example, if you are tracking at the sidereal rate with a 30% guide rate, the guide pulses will cause the mount to track at sidereal +/- 30% in RA, and at 30% of sidereal in DEC.
It is possible to set the guide rate to 0%, which has the effect of ignoring guide pulses for that axis. However, if PHD is sending pulses during a calibration run and EQMac is ignoring them for a particular axis, calibration will eventually fail since the guide star will not move. Therefore, it is probably best just to switch off guiding for that axis in PHD.
It is also possible to set the RA guide rate to 100%, which will cause tracking to stop completely for eastward guide pulses. For westward pulses the mount will run at twice the current tracking speed for the duration of the pulse. Of course, this will all be reversed if you happen to be in the southern hemisphere.
It is recommended to set a guide rate of around 30-50% so that guide pulses make very fine-grained corrections.
Once you have set the guide rates as desired, you should start up PHD and set the mount integration type to EQMac using the Mount menu. Click the connect button to get PHD connected to EQMac. Configure and connect to your guide camera and then acquire your guide star as you usually would. Please note that at the time of writing, you will need to download a special pre-release version of PHD. This version contains the support for EQMac, which has not been yet been officially released. The pre-release version of PHD is available from Craig Stark's website. You will need version 1.13.3 or above.
You may need to adjust the calibration step size in the PHD brain icon configuration dialog. During my testing, I found that a calibration step size of 2500ms worked well with an EQMac guide rate of 30%. However, your mileage may vary depending on your exact setup, so you may need to experiment here to get the best results.
When everything is configured, make sure EQMac is tracking at a rate appropriate for your guide target (typically sidereal for stars) and tell PHD to start guiding and it should begin its usual calibration run. If you look at the status bar in the main control window of EQMac, you'll be able to see the various guide pulses arriving and of course the guide star should be moving in the PHD window. When calibration is complete, guiding should commence as normal.
Finally, I should point out that EQMac will only be responsive to guide pulses if the mount is tracking. If not, then guide pulses will be ignored since it doesn't really make sense to be guiding but not tracking. However, if you've slewed to your target as normal, EQMac should start tracking automatically once the slew completes and everything should be fine.