Hi Choosing an Apps is higly depend on what you need , BEA weblogic is a full blown application server and its commerical with many features.you can not use if for deploying you application for commercial use.
Sun Apps 8.1 is free for use for commercial . Best way for you , IMHO is to get netbeans 4.1 which is boundled with Sun APPs 8.1 and use it to convert your application because it suports both Sun apps and tomcat + very good JSP and EJB development.
---- there are some other certified APPS like :geronimo from apache , JonAs , Jboss and other but i Suggest Sun APPS if you want a free. ---- for resource : if you do not know EJB then take a look at SUN j2ee 1.4 tutorial available in sun j2ee site.
for using NetBeans for j2ee developing ,there is a very nice and handy book from netbeans.org which you can get freely.
If you want help from someone here, you need to post the error (otherwise all anyone can do is make wild guesses). And if it is an error with NetBeans, you will get a better response if you post you problem in the IDE's forum.