I have some data that I want to store in the DB2 9. Should I store this data as XML schema or relational schema?

This depends on the data you want to store in the database. The main difference between relational schema and XML schema is that relational schema describes data as strongly structured and typed. XML schema describes data as loosely structured and typed. XML schema describes data order, but relational schema does not.
In general, data that has the following properties should be stored in XML:
The data is better described in hierarchal format.
The schema is constantly changing and evolving.
Many attributes of the data are empty or unknown.
You can check http://www.ibm.com/developerworks/xm...GX06&S_CMP=EDU for advice on creating XML.

The data which I want to store in the database contains small amount of data, but have a highly complex structure. Should I store this in XML data type?

You should store such data in XML. If you store such data in relational tables, you will have complicated relational schemas, which means you require many tables. Managing these tables can have overhead. The SQL query to access such data requires joining many tables. If you have to process this data together with other data, the SQL query will be even more complicated.

Is there any way to validate the XML data against a XML schema before inserting into the database?

DB2 9 supports validating XML documents with XML schema at insert or import time. The XML schemas have to be registered in XML Schema Repository (XSR) before it can be used for validation. The XML document in the same XML type column can be validated by a different XML schema of your choice in the insert/import time. You can also choose not to validate the XML. In general, there are three choices:
Validate on the server.
Validate within an application.
Do not validate.
XML validation enables you to create complex rules that define acceptable data. You can check http://www.ibm.com/developerworks/xm...ary/x-tipxsslt to use the XML Schema Standard Type Library to simplify the process of requiring formatted data such as e-mail addresses and telephone numbers.

I know that we can validate the XML data against registered XML schema. But how does DB 2 manage XML schemas in general?

Applications can choose to validate XML documents against an XML schema to ensure valid data is stored in the database. To validate documents, DB2 needs access to the appropriate schema information. For this reason, DB2 has an XML schema repository (XSR) that maintains a copy of the XML schemas that might be used during validation. The XSR consists of a set of new catalog tables together with commands, stored procedures and APIs to register and manage XML schemas. You can check http://www.ibm.com/developerworks/xm...y/x-style.html for defining data validation rules in XML schema.

do I have to register a XML schema in XSR before using it for validation?

Yes, A XML schema has to be registered in XSR before it can be used for validation.