I need to add some 3rd party APKs to my AOSP build. What folder should I keep these APKs so that when I build the code and the image is created, it is installed in the emula
You could also do the following in the target output dir:
/host/linux-x86/bin/simg2img system.img temp.img
mkdir system_root
sudo mount -t ext4 -o loop temp.img system_root
At this point you can make whatever changes you'd like to the files in system_root, i.e. adding apks to system/app etc...
When you're done just go back down to the output dir and do:
sudo umount system_root
/host/linux-x86/bin/img2simg temp.img system.img
You can now flash system.img using fastboot as usual.