Changing the look and feel of a program is as simple as :
UIManager.setLookAndFeel("fully qualified name of look and feel");
before any GUI creating code has been created. So you can easily create all your GUI with your GUI builder and the simply call this at the start of your program.
(Note that some look and feels like Substance are very strict when it comes to Threading issues so you better make sure that all your GUI code is run from the Event Dispatching Thread)
As a suggestion, two very good looking (and professional looking enough) look and feels in my opinion are Substance and also Nimbus which will ship with later releases of the JRE as the default lnf (at least that's the plan) and which can be downloaded separately from java.net
So if you opt for Nimbus the code would be :
UIManager.setLookAndFeel("javax.swing.plaf.nimbus.NimbusLookAndFeel");
And one example of Substance (Substance has many skins and themes, if you want to know more read their documentation in their site) would be :
UIManager.setLookAndFeel(new org.jvnet.substance.skin.SubstanceBusinessBlackSteelLookAndFeel());
Also note that you can use the cross platform skin (Metal) like this:
UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName());
And finally if you are on windows you can use the system look and feel like this:
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());