...? When a chapter end you have to reopen the emulator and select the chapter you wanna play. I don't see the problem. You can't reopen the emulator? You can't select chapter 2 specificly?
Nah don't worry. But having in consideration I can't help you cause I don't really understand: Check this gameplay and how he access to the Chapter 2
Minute 22:02 (When he's on the Fake Computer, just reopen the emulator "isaac_beta02.exe" and select the chapter he wanna play. Its the same with every chapter.