How to monitor the performance of a mysql database during development?
My favorite monitoring tool is the slowlog, with long_query_time=1.  And use pt-query-digest to summarize the results.  Then work on improving the first few queries in the list.  They will, by default, be ordered with the "worst" queries first -- either slow but infrequent or fast but frequent (or both).

Digging into why a particular query is slow (or frequent) may lead to a missing index, the need for a 'composite' index, reformulation of a query, redesign of the code, tuning, more RAM, or any of a dozen other things.

More here