Hi Cesar
If you want to extract only specific chart of account GL accounts into BCS. Please check the configuration under Load from data term method under mapping for FS Item maintain condition and reassignment to extract specific Chart of account GL accounts.
Please consider below link :
http://help.sap.com/saphelp_sem60ep1/helpdata/en/f7/726b40dde0980ae10000000a155106/content.htm
Regards
Rajesh SVN