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Two Offices sharing Projects

I have 2 Offices who will have their own QuickBooks and are in different time zones.

They will both work on the same projects and thus reports must cover both offices.

Do I create two "Companies" that will appear in the drop down on the top RHS? Or do I use a single company and then have the users adjust time zones individually under personal preferences?

Here you have to make a decision. If you want to keep these two companies separate, OfficeClip allows you to have two instances of its software from a single installation. In this case you will create two organizations and select between the two like what you described above. If you do this way both companies will remain separate and their QuickBooks sync will not interfere.

OK, but will both organizations access the same projects, or are they totally independent?

I need to have all employees working together and appearing on project reports so maybe one organization is required.

In that case use only one organization and when doing sync with QuickBooks, select appropriate users in both addin. The QuickBooks interface of one system will only sync with one set of users and the other will sync with the other sets of users.