When you use ESTIMATE you can define sample size as percent or rows while COMPUTE analyze all the rows for a table.
Generally ESTIMATE results are very close to accurate.

You need to analyze your tables and indexes separately or you can use DBMS_STAT package to analyze entire SCHEMA or DATABASE.

The parameters to use CBO are FIRST_ROWS and ALL_ROWS but usually it is not set in the init.ora instead the default setting CHOOSE is used. When your optimizer mode is choose Oracle usees CBO if the statistics for the object is present else it uses RBO.

Sanjay