Could you be a little more specific? Which adapter did you install, the sample from SAP? Or a third party adapter?
You can get at the JNDI name through the Adapter metadata file which is loaded at config time, but I would not recommend changing it unless you have good reason.
As far as I know the JNDI has to follow a particular pattern for a JCA adapter to work in the AF, and so you can't "configure" it really, it is either correct, and the AF will be able to do the lookup of the ConnectionFactory, or it is not correct, and it won't. I think the format is pretty much : "deployedAdapters/<adaptername>/shareable/<adaptername>" and can't be altered. As far as I know that is, but if anyone knows better please correct me!