I have a windows desktop and use PUTTY to connect to a Linux server which is a pretty beefy machine. I would like to run BOINC on the Linux server to work on the MilkyWay@Home project, but im not finding an example of how to do this.
I have BOINC manager running on my Windows desktop system.

Depends highly on the Linux server distribution.
But even without that, you can see at http://boinc.berkeley.edu/wiki/Installing_BOINC#Installing_BOINC_as_a_package how to install BOINC from Linux repository (one built for that Linux, compatible with its libraries).

http://boinc.berkeley.edu/wiki/Client_configuration#Command-line_options and http://boinc.berkeley.edu/wiki/Boinccmd_tool show all the commands with which you can control the BOINC client from the command line.

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So far, I have the following installed:
1) /usr/bin/boincscr
2) /usr/bin/boincmgr
3) /usr/bin/boinccmd
4) /usr/bin/boinc_client
5) /usr/bin/boinc

When I run the following command as suggested by the link I get the following:

/usr/bin/boinccmd --get_project_status
can't connect to local host

Thanks, I think I got it running, but it's not using all the cores.

17-Apr-2015 10:06:44 [---] Processor: 128 GenuineIntel Intel(R) Xeon(R) CPU X6550 @ 2.00GHz [Family 6 Model 46 Stepping 6]
...
17-Apr-2015 10:06:45 [Milkyway@Home] Requesting new tasks for CPU
17-Apr-2015 10:06:48 [Milkyway@Home] Scheduler request completed: got 0 new tasks
17-Apr-2015 10:06:48 [Milkyway@Home] No tasks sent
17-Apr-2015 10:06:48 [Milkyway@Home] This computer has reached a limit on tasks in progress

Only 50 out of 128 cores are running... Is there a way to get it to use more cores?

Yes, it has 8x of the X6550 processors. HP DL980 G5 box. Each logical core is only 2Ghz though, so total of 256GHz on the box.

I ran boinc_client with the "--allow_multiple_clients" option referencing 2 projects, but it's still only running one instance. The second one just terminates.

boinc_client --allow_multiple_clients --attach_project http://milkyway.cs.rpi.edu/milkyway/ key
boinc_client --allow_multiple_clients --attach_project http://setiathome.berkeley.edu/ key

Specifically, the error on the SETI project is:
17-Apr-2015 10:48:11 [---] GUI RPC bind to port 31416 failed: 98
17-Apr-2015 10:48:41 gstate.init() failed

Guys, really, please stop posting account keys on the forums. Whether it's the weak or the strong account keys, doesn't matter. Just don't.

With the strong account key another user can take over the account.
The weak account key may be less of a problem, but still, let's not make it easy on others.

I'll leave the other posts with the weak account keys in view for the moment, unless usao wants me to hide those as well.

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Sorry about that. I come from a bitcoin background where someone having your key wsan't a bad thing, just meant they could mine to your account and you get the benefit.
Ill remove the keys from the posts I can find.