http://afkmods.iguanadons.net/index.php?/topic/3750-wipz-tes5edit/Is still actively being developed in this one of most powerful tools for modding. I've linked to the beta or alpha version because it is stable
http://www.nexusmods.com/skyrim/mods/1840/?or/and http://www.nexusmods.com/skyrim/mods/1334/? Ones not necessarily better than the other. I use them both Wrye Bash for Bash patch and Mod Organizer for managing mods as it easier/faster on an SSD then Wrye Bash.
BOSS has been depreciated and been replaced with http://loot.github.io/ I would recommend looking in the Bethesda forums Loot thread for the latest Alpha version.
As for merging mods I'm not an expert but I have success using http://www.nexusmods.com/skyrim/mods/37981/? for TES5Edit. The main page has instruction to install and use the scripts for merging. xEdit definitely takes a lot of hard work out of merging the old-fashioned way, but I would review merged mods using TES5Edit to check for inconsistencies.