By default, no, custom homes don't count as homes that spouses or housecarls will know to return to. There are a number of mods however to do it though. I think I'm using like three mods that all let you do something to that effect:
- Ultimate Follower Overhaul: http://skyrim.nexusmods.com/mods/14037
Has a "relax" option that essentially puts them on an idling standby. Not entirely the same as a home, but they'll interact with nearby objects like sitting in chairs (eating, drinking, reading, etc.) or using crafting stations.
- Spouses Can Live Everywhere: http://skyrim.nexusmods.com/mods/11370
You get a spell that sets the current location as "home." I haven't really messed with this much since it's sadly only limited to spouses, it does nothing for other companions.
- My Home Is Your Home: http://skyrim.nexusmods.com/mods/18045
This lets you set any followers home location through a dialogue option. They'll return to the location you set, and roam about it like they would a regular home. How far depends on how big the home is and where you told them their home was.
Using either/both UFO/MHIYH you can set followers to stay in the same location. I had 5 followers staying in my custom home in my last game.