Well that sounded helpful... The simple answer is, yes. He you install
a kernel update you custom kernel is not lost but will usually not
boot to it by default. When an update comes out, get the source and
build that then install the new custom kernel. If I was at home, I
would send you a link to building a package with your custom kernel in
it. I am not though, Google 'kernel ubuntu way' should give something
helpful for you.