By "emulator" you mean opening xephyr window and typing "af-sb-init.sh start" in scratchbox window? I don't think it is possible to flash any custom kernel there, because:
1. You compiled your kernel for armel architecture and your computer is x86 or x86_64 architecture
2. "Emulator" - above command - cannot (at least not when I tried it last time) be executed in armel environment, only in x86
3. When it is run in x86, it uses (somebody correct me if I'm wrong) kernel from your Linux host (from Ubuntu or Fedora or whichever Linux distro you have), it just fakes being a device emulator and runs whole Maemo software just like any other software on your computer (like web browser, text editor, etc.) giving you fake impression of being an emulator. These aren't even actual program packages which we have on our devices - these are their special versions compiled for x86 architecture (when someone uploads source to extras-devel, it is automatically compiled for both architectures resulting in two packages - one for actual devices and one special for scratchbox environment).

If you want someone to help you test your kernel, upload it here (image file and modules). On device it is quite easy to have multiple kernels installed - one just has to install multiboot, then put kernel in /boot folder, modules in /lib/modules and create special entry .item file in /etc/multiboot.d . I had never even dreamed of a device with boot manager capable of booting multiple kernels as easy as on full-size computer

So, wanna upload your kernel with short description what you had changed?