OEM Organizing?

[iljacksoniii]

Hello fellow members. This will be my first post so be easy on me ..Ive been on this site and xda for about 2 years now and im finally getting into cooking my own rom. Yet I prefer to do this from scratch, rather than just download a kitchen change a few packages and call it my own. I've actually been doing a lil cooking already. Xip and Sys porting, making my own oem, reg entries, alot...lol. Yet i just cant seem to organize my oemapps into their own seperate packages. Dont worry i have searched my a** off and still cant seem to find a tutorial or some instructions on how to do that on my own. Ive read about going thru the initflashfiles yet that file doesnt seem to cover all the files with in that folder. So im just asking if anybody can help me understand the process of which some of you Expert chefs go about doing this. Or at least point me in the right direction for the information I need.
Thanks and Love what you guys have been doing with the site over the years. Lots of helpful info.