I'm no user, and just discovered multigateway, I've read their docs, using my understanding, it seems that when you deposit Bitcoins (or anyother coin) to them, they create a new Bitcoin (or anyother coin) address for you only for which they hold the private key.
You  would [/edit] therefore monitor, that your mgwBTC amount match exactly the coins at the public deposit address, at all times (just give it a little time for transactions to settle). If this is true for any anounts and at all times, they are not doing fractional reserve.
 If they transfer the coins on the deposited address to another address (which is a better practice (see below)) you can't prove anything for sure, as you have no vision on the total of mgwBTC in circulation (and issuance process), nor can you know for sure that they really own the public address, and not for example rent some payment services from an address which has lot of bitcoin to inspire confidence (unless their whole book is public (and proven so), you then aggregate all transactions, see where the funds are coming and check it started at 0 and everything adds up the way it should)[/edit]
But a word of caution here, them not doing fractional reserve is not an all risk guarantee. It may even be considered bad practice. Their keys may get stolen at any time. All coins are 'live' (because of the no fractional reserve guarantee), this means if they get (self?) hacked, 100% is gone almost instantly. Whereas exchange usually have most of the cash on frozen addresses, whose private keys are not stored on a device connected to internet.
If there is a bug in their system, and for example their transactions are not really 'transactional' which is kind of hard to do in a distributed system and some mgwBTC got double spent, their transaction algorithm will automatically adjust your BTC deposit to match the mgwBTC. Which means if someone can steal some mgwBTC they can steal your deposited BTC.
An other word of caution: they seem to only release binaries of their software, which is not good for inspiring trust (but they are still beta).