If wanting to just change margin or padding there's no need to alter the XMLs (they don't handle this at any rate), but instead simply add the CSS to the bottom of your Joomla or CB template CSS file (or CBSubs template CSS file, whichever you decide). If you could provide a screenshot of how you're wanting changes applied as well as link to your live site (can be through PM) would be glad to suggest some CSS changes for you.

Since CB support custom template, I can just put CSS to modify CBSubs there as well?

Yes, as instructed in my previous post you can place the custom CSS in your Joomla, CB, or CBSubs template CSS file. This depends on how your CSS selectors are built. If not built correctly your CSS could get overridden.

I don't like editing any of original/core files because it's easy to forget which files have been modified during upgrade. At least I can copy/save the custom CB template folder for backup purpose.

I recommend adding to your Joomla template CSS file as it's less likely to change over time (generally once a stable template is installed it is rarely re-visited).