One approach would be:
SELECT SUM(x.amount) AS total_amount
FROM (
SELECT DISTINCT ssm.stid,fm.classid,value,fm.Amount FROM [bitcrj_database].
[StudentSubMaster] as ssm inner join [bitcrj_database].[tbfeemaster] as fm on ssm.classid=fm.classid
CROSS APPLY [dbo].[fn_split_string](ssm.subjectid,',')
) x