Photometry for eclipsing binaries is not different from other stellar photometry. In fact, as mentioned, most reported ToMs are from untransformed differential data, which simplifies the process. However, because you might have hundreds of images from one night, all of the same star field, you will appreciate having an automated procedure that does not require picking stars with the computer's mouse on more than a few "starter" images.
The software package AIP4WIN provides suitable automation, and is a popular, low cost, and effective choice (see the Software Resources page). The AAVSO offers VPHOT to its members, an online tool for performing photometry. It requires an internet connection suitable for uploading all your FITS images.
The tools used by professional astronomers (IRAF, Starlink, wcstools, SeXtractor, etc) are freely available. They run most easily on Unix/Linux systems. The learning curve can be steep, but they can be fully automated using shell scripting. The writer of these pages uses a combination of programs from of all these packages, assembled before the more user-friendly tools like AIP4WIN and VPHOT were available.