We use Salesforce, Freshbooks, pivotal tracker, and toggl:
1. Sales tracks opportunities and estimates hours with engineers
2. Sales creates a project in Freshbooks via integration from Salesforce when the deal is close enough to track hours
3. Freshbooks creates a pivotal epic and label with the Freshbooks project id - we estimate with a custom scale of hours (/me dodges thrown rocks)
4. When a dev starts a pivotal story it is automatically synced to toggl so they can track hours against it
5. The toggl and Freshbooks data is all syncd to Salesforce for roll up reporting and estimate vs actual reporting and our ops person pulls out all data from there to create invoices (some projects have weird parameters, so just using Freshbooks hours into invoice doesn't work for us)
Toggl is nice because it is user friendly and fast so you don't feel like logging time slows you down.