Organizing Stored Procs and Views
We have all been there. It sounds like you don't have a specific question, but just need some help getting started. You need to learn about the sys tables available in SQL Server and the DMV's. They are insanely useful.  

Ones that will be helpful in your case: 


sys.procedures - gets you a list of your stored procedures
sys.object - gets a list of all objects
sys.dm_exec_procedure_stats - gives stats of your stored procedures, how many times they executed, when the last execute was, etc. 
sys.dm_sql_referenced_entities - returns entities that are referenced by the object you provide (pass a stored procedure name and it will return all the tables and views it hits)
sys.dm_sql_referencing_entities - returns entities that refer to the object you pass (pass a table name and it will return all the stored procedures that hit that table)