Hi Luis!
I am really sorry that X-Cart 5 does not quite meet your needs in terms of functionality. I will do my best to help you with this issue.
Yes, indeed, Tracking numbers is not included into default X-Cart 5 and if we will be happy to consider them for future releases if you upvote it here:
http://ideas.x-cart.com/forums/229428-x-cart-5-ideas/suggestions/4860334-tracking-number-field
Besides that, even without official release of this feature, I will be glad to help you write a mod that implements the essential part of this functionality. If you are OK with that, please let me know and we will discuss what can be done.