In the person object, I have a department reference attribute. I need to flow the department values from a sql table to FIM department reference attribute. In the  CONFIGURE ATTRIBUTE FLOW, I have dept(sql- reference) to dept(reference - Type direct/object type - person). but how can I let FIM know the flow is of department object?

If it is a reference in SQL, it can be resolved by Management Agent.

In its Properties, in Configure Columns section, find the attribute you want to specify as reference, select it and click Edit button. Then tick that this column is "Reference":

Then, just flow directly this value to metaverse's reference attribute.

You have to have referenced object also available in the table/view that is accessed by this MA. According to TechNet Article:

If a reference column is used, you must also use a single anchor column. In certain cases, to guarantee a unique object identifier, you must also create a separate column that contains an identifier (such as employeeID) with an additional column containing the object type.

Please see here:

http://technet.microsoft.com/en-us/library/cc708679(v=ws.10

I have that already. After FI, the preview has the import atribute flow - final value as deleted.

a)The object type of the anchor(person) is different from that of this reference attribute(department). Does it matter?

b)searching the connector space of the sql ma, I could see a place holder for the department object.