One of the goals for the rewrite of the tools was to allow greater matching or sources and sinks. Meaning different inout sources and Output sinks. Inputs can be JDBC, hbm.xml, annotation classes etc See
http://www.hibernate.org/hib_docs/tools/reference/en/html/ant.html#d0e710. Outputs can be POJOs, hbm.xml, DAOs, HTML, etc. See
http://www.hibernate.org/hib_docs/tools/reference/en/html/ant.html#d0e796.
We do this through a standard meta data datastructure. Fortunately, hibernate has one it uses internally so we have used it for the tools (hence why it more critcal to use the correct tools built to the hibernate built but Im going off topic).
So what does this mean for you. Notice in the example I provided that you have an input stream which is a configuration. In your case you need to use the <jdbcconfiguration> since the input stream is the db meta data. Then you set the output stream. For example you use the <hbm2hbmxml> exporter to generate the hbm.xml files. You can use multiple exporters.
In the case of controlling the <jdbcconfiguration> you can set properties in the hibernate.reveng.xml file. See
http://www.hibernate.org/hib_docs/tools/reference/en/html/reverseengineering.html. This allows you to control the process of tables etc to read and many other aspects. The section of the docs I have linked to will explain it all.
Hope this helps.