.htaccess question

Q1. Normally yes. If you are addressing /codeigniter/ then rules from the route .htaccess will apply, and can be modified or further rules applied by the .htaccess file in the /codeigniter/ folder. A CI remove index.php htaccess should be in the CI root folder, in your case /codeigniter/
Having said that it all depends what you are doing. You can apply rules in the route .htaccess for other subfolders too.

Q2. You can change the webroot for Xampp (assuming you are using that) in their config files. Here is a handy stack overflow answer about it: http://stackoverflow.com/questions/18902...-directory

Personally I would not do this, but just accept that in development locally you have the additional folder in URL's. If you set your base_url in the config this is just one setting to change when you upload it to a live site.

Hope that helps in some way,

Paul.