Since many people have trouble setting up a merged mining pool, we'll describe typical workflow for merged mining pool is like this(suppose we are mining LTC and FSC)

The straum-mining server part:

Update job:
call "getblocktemplate" from LTC
call "getauxblock" from FSC
insert some special script into LTC's coinbase
generate job for stratum miners as usual

Upon receiving a share:
If it meets our diff: log that share for both LTC and FSC
If it meets LTC diff: call "submitblock" from LTC
If it meets FSC diff: call "getauxblock" from FSC, but this time we need to prepare some arguments so called auxpow.

For how to insert into coinbase and how to solve a block using "getauxblock", you should check out https://en.bitcoin.it/wiki/Merged_mining_specification
I'll briefly describe it here:
1. script into coinbase:  'fabe6d6d'+getauxblock['hash']+'01000000'+'00000000'
2. build auxpow: coinbase_hex       + parent_hash + branch_count                + branch_hex                      + "000000000000000000" + parent_header
                       hex of coinbase    litecoin hash    count of merkle branch        hex of all merkle branches                                         litecoin block header

MPOS part:
Of course another thing to do is patching your MPOS to display two coins, and add scripts in cronjob to handle payout of FSC.

Wish it would help, we'll also release a forked version for python "stratum-mining" and php-mpos, you can check it out.