Hi,
Special GL indicator is mainly usiing for Customer Down payment and vendor downpayment. U have to set the configuration in OBXR & OBYR t.code for them.
once u set the configuration there, then u have to select the (put tick mark) in Special GL transaction in Vendor and Customer line item dispaly (FBL1N & FBL5N). then it will given the Spl indicator as "A" for downpayment of customer and vendor
Special Ledger Definition - ERP Financials - SCN Wiki
Regards,
Sanju M S