Handling Multiple chart of accounts

An organization has three projects, p1, p2, p3. An employee is giving his time to all these three projects, thus, he/she is getting salary from the three projects. Lets suppose, we have three different chart of accounts, for three different companies, then how we are going to manage the salary of this particular employee. The reason is that, in the hr.employee tab i.e.accounting, there is only company payable, company bank and employee expense account mentioned. It is some how very diffiuclt, if we need to have multiple accounts for the same employees. Any hint will be highly appreciated?