I am going to help you B4 U get hit with the ADD YOUR SPECS TO YOUR SIGNATURE bit.
No one will ever help you unless you follow rules and start trying to do for yourself.
So,
Logo and head of store etc is all in your skin1 file folders. Read the manual as this should (I never did) show you where to go for everything.
Logo is all in skin1/head files. There are several depending on the version of yuor store yuo operate.
Example head.tpl, head_printable.tpl, and head_admin.tpl . All of these need changing. Also if you have the affiliate module, then you will need to do the head_partner.tpl also.
For the invoice logo, go where the invoice is: skin1/mail/html/order_invoice.tpl
NOW, go to Forum FAQ's
http://forum.x-cart.com/viewforum.php?f=27 and read all of the main topics. These will answer most of the NEWBIE questions you will have.
Beleive it or not, I hear the new manual also answers questions to most people's satisfaction. It used to not be worth the ePaper it was written on, butr now is supposed to be pretty good. I learned the hard way, mostly without help and never had a good manual, so I cannot tell you as I have yet to crack a good manual from them and now do not need one.
Don't forget to add your details in the signature or no one will ever answer you.