There are a couple of ways you might approach this:
Have users track time at the project level. This is a Project Type attribute that will give users one line item on their Timesheet per project, regardless of how many actual Tasks they may be assigned. This is the easiest to administer in general, however this only allows for time tracking at the highest level of the project and will not give you the granularity of work packages within the project plan.
The other option is to create a Task representing each work package the user may be assigned to on the project, then leave the actual detailed tasks unassigned for the PM to update status and progress. This means the PM will have to add a Task line item for each work package for the purposes of time tracking, which may throw off Planned and Actual work rollups, but it affords the granularity of time tracking you may require. One thing to be careful of with this solution is that if you have multiple resources assigned to the same work package task, the Planned Work, Actual Work to Date and ETC or % Complete on each user's timesheet represent the aggregated total for all task assignees, so users need to be instructed in how to "co-manage" these shared tasks.