Take a look at the Expert settings. You have to edit them anyway. It doesn’t matter how you have installed Win95 and AoE, as long as it’s working. If you have e.g. installed both on a single image file, it’s perfectly okay. But you’ll have to adjust the -size parameter, because your image will have a different size than mine, if both Windows and AoE fit onto it.
If Dosbox is stuck on “boot c”, it’s usually a sign that the -size values are wrong. Here are the correct values for different hdd image sizes:
32MB: 512,63,16,520
256MB: 512,63,16,520
512MB: 512,63,32,520
1GB: 512,63,64,520
2GB: 512,63,64,1023
If you want the according empty hdd images, get them here.