Included with mastercoin-tools are 2 different methods for downloading/updating the blockchain information.
Continuous running application that you can start in a screen session. It will download/process the entire block chain and then sleep for 60 secs before checking for updates.:
screen -R msc ./app.sh ctrl+a, d <disconnect screen> reconnect at anytime with screen -R msc
Alternatively you can schedule a cron job to execute the msc_cron.sh utility at your predetermined time.