Hello,
well, the format of URLs used by JoomSEF is very configurable, so you have several options:
1. either you make it to generate exactly the same URLs as you had before (this depends on the format of URLs you had so far)
2. you adjust the URLs manually (that is perfectly possible in JoomSEF)
or
3. use new JoomSEF URLs and define 301 Redirects from old to new ones
As regards compatibility, there is a list of extensions available:
http://www.artio.net/en/joomsef/artio-joomsef-extensions.
Jomsocial is listed there as regards Jfusion, I am not sure about that one. However, in case it would cause problems you can simply disable the JoomSEF functionality for this single component.