Check out the criminal indictment if you are interested, they explain it a bit.
From memory (which may be wrong), it sounded like he had something like 11 internal hot wallets, but while the coins were in escrow he used a database to link what user had what amount of coins. The government seized those 11 wallets, and based on the average daily holdings, now have like $3mm worth of BTC which they transferred to a single wallet (if you google, you can find the public record of that govt controlled wallet).
The indictment also explains that Silk Road used a "tumbler", which would route the BTC's through a series of random wallets so that it was not possible to match a user's initial sending of BTC to Silk Road with the eventual withdrawal by a seller of BTC's to another wallet or exchange.