Setting up a Marketo partition to sync with a SaleForce Partition

You probably mean Data Divisions in SFDC.

As far as I know, Marketo does not know in whatr division the data is and cannot mange the fact that it inserts data in partition, vs another one.

This will have to be managed through workflows in SFDC, on lead creation or update. You will have to pass the Marketo partition name to SFDC, so you need to create a "Marketo Partition" field in SFDC and sync it with Marketo. Then you need to run a smart campaign in Marketo that populates that field with the name of the Marketo Partition on lead creation or each time the partition is changed.

The you will have to create a trigger, a workflow or a process builder that fires when the lead is created or each time the "Marketo Partition" field is updated and moves the leads to the proper division. I would recommend triggers, in order to avoid any issue with governor limits in case of bulk updates.

You might also want to prepare the case of a division change in SFDC that should cause a partition change in Marketo.For this, you need to update the "Marketo Partition" field when the division is updated in SFDC, using an SFDC workflow, Process builder or trigger (again, triggers preferred). Then some smart campaigns in Marketo that detects that change coming from SFDC and moves the lead.

Last but not least, the help of an experienced consultant that knows Marketo and SFDC well might be helpful.

-Greg