2-part htaccess questions

Zen cart requires register globals to "off" and if the server will not abide, they offer this as an htacess:

php_value session.use_trans_sid off
php_value register_globals off
#php_value register_globals off
<Files ".ht*">
deny from all
</Files>

I built the file and uploaded it and then it disappeared. Come to find out it was there but I just could not see it. If you upload again it says that you will rewrite that particular htaccess file so you know it's there.

Question #1. How do you know that you are not going to overwrite another htaccess file in a different situation if you cannot see the file?

Joomla comes with htaccess files and most times Joomla is installed into a folder and then I guess there is a redirect set up if you want it to be your default page/program when your main domain url is type in.

I have been installing Joomla into the root folder for years?

Question #2. Does this mean I am compromising my security by installing the program and the included htaccess into the root so that the program opens when my domain name is called?

These are not pressing questions at least not until I go to install Joomla and Zen cart again. Thanks for any response, especially if I am nit-picking.

To disable PHP's session use_trans_sid I was told to add this line to the htaccess file:

php_flag session.use_trans_sid off

Is the above code the same as below:

php_value session.use_trans_sid off

Is there a difference between flag and value?