The JForce 2.0 extension will allow you to create quotes and invoices and associate these with companies.  Quotes and Invoices do not have to be tied with projects, but can be, for better organization- if you want.

Quotes can be setup to automatically generate any number of invoices with the amount being split equally among the invoices. Quotes can also be set to publish and unpublish at whatever particular times you specify.

Invoices provide an exceptionally easy way to secure payment from contacts, and the system has been written to handle any type of payment gateway through an incredibly flexible plugin system. Both quotes and invoices can be emailed or printed as well as viewed online for ease of use and record-keeping. You can accept payments easily and securely on your website using a variety of payment plugins. By default the system includes credit card processing (through Authorize.net) as well as PayPal payments and a host of other plugins can be written for the processor of your choosing. Your clients can view only the quotes and invoices that have been assigned to them and make payment securely directly on your site.