bulk logged is the best mode to control growth during index rebuilds, then a full backup afterwards. Note log backups will still be large though. You could also try backing up the log more frequently during reindexing.

You are correct to try and only rebuild indexes that need it, the dmv for that is sys.dm_db_index_physical_stats. This will also reduce log activity. There are many scripts for that, I enclose the one from BOL which works just fine plus the crowd favorite is Olla Hallengrens suite of utilities for maintenance.

For those indexes which are only reorganised you will still need to update the stats.