First of all: I don't bother much about being 100% Scrum compliant, or any methodology, so the following method might arouse some comments from those who follow a methodology to the letter. I unscrupulously steal every good idea, whatever the source, as long as it fits good project management practice.
First build the WBS of your project up to work package level. Then design the plan or work package network the way you want to build the product. After estimating, this network goes into MS Project for scheduling.
The work packages represent the Product backlog. Based upon your schedule, you can devide the duration in sprints or groups of sprints with intermediate results (iterations). This depends upon the product you are building and/or the way you organise the project to track progress (increasing product maturity).
Each sprint the product backlog items are translated to a sprint backlog. From then on it is the normal Scrum proces at work here. Time is tracked against work packages and together with physical % complete and/or ETC can be fed back into MSP or any other 'system' for reporting and forecasting.
Although we're far from big design up front, as some may call it, you do need to have a pretty good idea of what done looks like. But hey, that is sound project management, right?
So the work package network rarely changes (unless increasing understanding leads to an improved plan), but flexibility is allowed within the work packages, depending upon the feedback of the customer after each sprint.
Based upon your WBS and network and the size of the project, you can have more than 1 scrum team working in parallel, each team assigned to a single (big) work package or (usually) a group of work packages leading up to a specific result.
Not all the work packages have to be done by using scrum; typically only the development stuff is organised this way. If you have other work to be done as part of the whole project (like training, transition to business etc.) these may follow another 'method' of realisation. As always, it all depends ...
Hope this is usefull.