Nate
Having just been through the same issues, I will try to explain. The functions you need for astrophotography are:
Camera control -Backyard EOS (BYE for short)
Guiding - PHD
Go To and other mount controls - EQMOD
The distinction between tracking and guiding is often not well understood, after they sound similar. Tracking the the mount mechanically following the movement of an object. Guiding is using a star to make corrections to that tracking to compensate for small errors in polar alignment or the mounts mechanics.
The software interacts in certain ways. For example you can get Backyard Eos to interface with PHD to introduce dither. This means after BYE completes an exposure it sends a command to PHD to move the mount slightly. This is helpful to help reduce the noise during stacking. Also EQMOD can control PEC (Periodic Error Correction) slightly changing the rate at which the mount tracks to reduce errors in the RA mechanism. It achieves this via an interface with PHD.
To answer your specific queries, BYE will not move the mount. If wanting to get the mount to point you will need EQMOD (or you can use the handset on the mount). Be aware that EQMOD is not really a "program" as such. Rather it can be thought of as a set of drivers that allow another program, such as a planetarium program like Cartes Du Ciel or Stellarium to talk to you mount. It does extend the functionality that a handset has. For example you can use a wireless gamepad to control the mount, directly slew the mount from your laptop, and lots more.
Backyard EOS is a great program. There is a good video here
https://www.youtube.com/watch?v=z3gkw8bx7Aw that explains many of the features (be aware it is about 2 hours 40 minutes long!) by the programs designer. But it is esesntially a camera control program.
As to what you "need", PHD is really the only one you really need. I did quite a lot using the handset and running the camera with a cable release. But EQMOD and BYE automate a lot of that and you can do a lot without getting out of your seat.
Malcolm
