Well like i said, you can manually call the controls into your template.
Although i'll tell ya, i haven't ever been limited by going pure Portal method, but i have with ASPX+Portal. I would always encourage you to look into doing things through Portal as it gives a lot of flexibility, if you need to do logic during the various Page Cycle events you still can through a custom control.
Good luck to ya! Ask if you have any questions on the webpart to api, i have more info on my devtrev.com site.