Just spent 3 months converting all of my firm's VAJ-developed/maintained applications running on v3.02 WAS to WSAD 5.0 (trial --- no money to buy yet, so hads to reformat and re-install) running on v5 iSeries WAS.
Some pointers. If your old applications used .properties files, you must decide how/where to loacte these. Our applications were simply Web applications, but still need both a WAR file as well as an EAR file. Just to prove concept, we placed .properties files in root of the J2EE Project, but later decided to read them from file system. To do so, use an <init-param>/localeof_propertiesFiles</init-param> in web.xml.
Legacy services like MQ Series and JDBC libraries posed another hurdle. Use WSAD Help to learn about "Using External Jars". A great idea of IBM was to provide WSAD Help on-line at: http://publib.boulder.ibm.com/infocenter/wsphelp/index.jsp
Using this site, you preserve resources in your WSAD workspace.
Use right-click on Project -> (and pick) Properties then pick Libraries. There are choices, here. To use absolute path locations, pick "Add External Jar". To specify more of a relative path pick "Add Variable". When moving from WSAD Unit-testing stage to WAS System-test stage, I learned that our AS/400 environment cannot deal with the drive letter specification required by Windows-WSAD. Roughly, on WAS 5 Admin Console, "Shared Libraries" roughly equate to WSAD "Add External Jar" and "WebSphere Managed Variables" roughly equate to WSAD "Add Variable" (sort of like setting a "Windows Environment Variable".
The Help files help a lot. The WebSphere Developer Domain provides plenty of Articles and Redbooks, but I found the Help files most helpful.
So far, I like using WSAD. Next we must install ClearCase LT.