I would like to change the default administrator username on my Windows Server 2008 R2 but not sure whether it would effect my environment badly or not. I am also connecting to my server with this account through remote desktop. Here is the step I came so far but didn't do anything further because I am not use;
Can I go ahead an change the username to whatever I want it to be? will the system need a reboot after this change?
There are no adverse effects to the OS itself. As mailq notes, internally the OS thinks of that account as 'RID 500', not 'Administrator'. I cannot speak for all possible applications, but any properly written app will be just fine with the change.
Really, the only predictable potential damage is to your future self, your present and future teammates, your potential replacement. Imagine coming upon this server a year in the future and saying to yourself 'I know I changed the Administrator account's name ... but what did I change it to?' Not being able to remember would be A Bad Thing. Windows has a convention of naming this account 'Administrator', and that's what everyone expects it to be.
Ask yourself why you're making this change. If you believe it provides some extra measure of security, you might want to re-think that. Adding a few bits of entropy to the password for this account would provide at least as much extra security, and leave the 'well-known default' in place. As a sysadmin, I find it's always wise to have really good reasons for changing defaults. Reasons I can clearly enumerate and justify if asked.
Sure you can change the name. This is only the "display name" and your user name won't change. So there is no need for a reboot.
I'm not sure what will happen if you try to change the username. The last time I did that on a desktop machine my Windows denied to change the username of the user currently logged in. So in this case I had to rename it from another administrative account.