Can I manually change my htaccess if I set password protected directories?
I need SEO freindly URL's and I doubt I can change this

I have seen that htaccess is modified if I change by software like CoffeeCup Access Manager.

1. Will this be interupted as password is set also by this sofware?
2. What is correct file to change URL's and htaccess?

One would think that CoffeeCup Access Manager does not overwrite the entire htaccess file since many things can be accomplished using htaccess that are beyond the capabilities of that program.

I have checked and htaccess is modified in folder where is defined security for this folder.

1. If I create htaccess, should I add lines of code in this file or change of security will change this htaccess?

From your post htaccess will not delete line of rewrite and so on...

2. If I create form under secured folder, what code to place in htaccess to redirect form for specific user which is logged and specied with application:CoffeeCup Website Access Manager?

Can be this redirect managed by CoffeeCup Website Access Manager or htaccess. How to do it in correct way?

3. Can I track logged users after I secure folder with CoffeeCup Website Access Manager?
Can be stored IP address, username, password?

Imagine you have 2000 users...

Can you please help me?