does anyone have instructions for using BAM with FreeBSD and configuring it from the command line?

I don't know about FreeBSD, so here are some "generic" instructions.
First download the sourcecode
As explained here, run this:

./_autosetup

./configure --disable-server

make

To administrate your BOINC installation from the command line, first start the client (using the 'run_client' script, I recommend you also use the -daemon switch). Then you could either use BOINC Manager from a separate computer, or use boinc_cmd.

A little note on boinc_cmd: attaching to a project using email/password is all but straightforward. Instructions:

./boinccmd --lookup_account http://project_url/ email@address.com passwd

This command will output something useless like status:0. Then run this:

./boinccmd --lookup_account_poll

It should give you a long alphanumeric string (the account key). If it doesn't, just wait some seconds and try again. Then:

./boinccmd --project_attach http://project_url/ account_key

And that should get you attached. You can confirm so with:

./boinccmd --get_project_status

I have boinc running and can see the box from the seti pages. However, when I execute

I copied acct_mgr_url.xml from a windows box and after executing

#boinc_cmd --acct_mgr_rpc http://bam.boincstats.com username password

acct_mgr_reply.xml & acct_mgr_request.xml were created

I can't see the box from boincstats.com tho.

You mean it's not shown here?

that is correct. acct_mgr_reply.xml is an empty file FWIW

Command-line support for account managers is quite bad, I looked a bit on the sourcecode and I don't even understand how the manager uses it. I suggest you use a graphical manager (from another computer) to administrate it. Command line support really needs improving. It's mostly just a crude frontend to the GUI RPC internals... Almost 1:1 matching with the messages being sent. That's far from user-friendly (as you can see on my instructions for doing something as simple as attaching a project).