If I am understanding the problem correctly: you want to show hard coded items in your sidebar.php i.e. Archives, Categories and etc. as well as widgets.
IF that is the case, I too found that the sidebar looked fine with just my hardcoded entries but when I added any widget like the calendar, recent post and etc, it looked bad. It wasn’t removed but it looked bad.
I was able to correct the problem by modifying the style.css and element settings around the widgets function in the sidebar.php.
If that is not the problem, then what MichaelH stated is the best help. Reading those articles helped me.