Db2 – How to find out what caused the database(DB2) in a locking state

when I explicitly lock a row or a table, am I employing the exact same constructs that are used by the database's transaction facilities under the covers to make the transaction work properly?

Yes. If that would not be true, then your own 'locking' would only be scoped to other similar 'locking' and not interact with the engine own locking. So you would lock a row in a table so that it cannot be locked by another application in the same manner, but your lock would be ignored by the engine itself. These semantics are seldom desired. Most of the time an application locking a row means 'lock it against any means of access/modify'. Side note that locking mechanisms that are strictly application specific do exists, because they are useful. For instance SQL Server has application locks.

it occurs to me that in order for a transaction to be atomic and isolated, it must be doing some locking.

Locking is one means to achieve this. The major alternative is versioning. Nowadays most databases support both (which also means that if you 'lock' a row in the app but another transaction uses versioning to read the row, it will read it because your locking does not block versioned reads).

You are sort of circling around a concept known in the database implementation world as 'two phase locking protocol'. the linked Wikipedia article is a good starter. If you want to read more detailed explanation about this topic I recommend head to the library and ask for a loan on Transaction Processing: Concepts and Techniques. Pretty much every database out there is, at its core, an implementation of that book.

I have the same issue on RDS. Some of "cleaning up" transactions blocked my ALTER TABLE query. And as I understood in MySQL 5.6 there is no way to find out which transaction should be killed.

So, my solution was to kill all "cleaning up" transactions. And it helped me. And more thing: according to AWS doc on RDS you should use CALL mysql.rds_kill(pid) instead of standard KILL.