This is a general comment rather than exact instructions but I hope it helps you:
If a piece of software is protected by FlexLM the vendor will normally supply the FlexLM server software when you buy their package(*). My experience has been in installing the windows version but I expect the concepts are the same under Linux. ( Looking at Altera's instructions
http://www.altera.com/support/licensing/setup/lic-setup-float-unix.html confirms this). FlexLM requires very few files, typically 4 or 5: A Windows Service/Linux daemon lmgrd, a 'vendor specific' daemon, a licence file and a configuration utility lmutil. Installation should be fairly straightforward, hopefully following the instructions origin give you and consists of copying the files to a directory on your server, modifying the licence file to match your server, then starting the lmgrd daemon.
The tricky bit for SME is any config required to allow the PCs on you network to reach the daemon running on the SME server and configuring the lmgrd daemon to automatically start on boot, so may I suggest you:
1) Read the pages here (assuming this is the software you need to licence)
http://wiki.originlab.com/~originla/wiki/index.php?title=Basic_Setup_Instructions. The Altera pages linked above also worth a peek.
2) Buy the software and get your licence file which will be tied to the MAC address of your server.
3) Come back with questions reqarding the specific quirks of an SME install.
4) When you suceed write it up here or as a howto to aid others in the future.
Regards, Mark Leman
*My experience has been with Altera FPGA development software and Mentor Graphics. Altera even make the downloads available on their web site.