Thanks for your help Kharvey and Rich, I have read persistence for dummies several times, but i still cant seem to get my head around this 'philosophy' of linux.
Going through the notes on executive summary: To make everything persistent, use the Set button in Appbrowser to set a location for /tce. If using the built-in installer, this is taken care of.
I am installing via the console using the 'ab' command and (i)nstall, is this equivalent to the 'set' button?
If adding the conf files to the .filetool.lst is the only way to do it, i will use that method, but if there is another method more old school where you just alter the .conf files or add files anywhere under the root directory and you expect it to stay there after reboot i would prefer to use that method.
Thanks again for all your help.