Changes in templates possible ?

Hi there,

this is a more general question using templates.

Is it possible to add some things (in this case html-links) to a template which is used for an ecommerce website ?

In case this is difficult to understand I explain a bit more:

I am going to add ecommerce functionality (login/registration, ecart, download center..) to an existing website. I am now pretty much in the final phase ... but just realize that I have to add a few links to the top menu. I only can do this by adding this to the template which is used for all the sites created by the security and ecart wizards.

Can this be a problem for all the sites I created and all this "dynamic stuff" ?
Or can this be done without concerns ?

I think I read somewhere - I believe this was as I worked with the "Validation Show If" behavior in the registration page - that if the template is changed the dynamic php code is lost or something like that ... (:

So, I just want to be sure that this don't will happen ... !

And would be grateful for any help and clarity about this!
Thanks ...

Henrik