How to make custom apps to appear by default in the lower dock panel in my custom ROM
You'll need to edit the apk for the default launcher, which in this case is TouchWiz launcher. You'll need to figure out how TouchWiz gets its default setting, my guess is it would be in some of the xml files in the /res/values/ folder for the launcher, which should make modding easier as you'll only need to extract the apk, edit the files you need, and recompress and probably resign the package but it may also be hardcoded into the code in which case you'll need to decompile, reverse engineer, and recompile the Dalvik class files in addition to the previous steps.

These are some tools that might help you do these modifications:


apktool: A tool for reverse engineering Android apk files
smali/baksmali: An assembler/disassembler for Android's dex format
jarsigner: tool to sign an apk (included in SDK)