First off, you're gonna want to have access to as many preps as possible, so make sure you've done a bunch of silver challenges - most of them have very useful item rewards - and upgrade all your buildings. Second, Vicious halls of steel is a lot easier than Naga city, I find. Some tips:
1. All the important enemies in VHoS use magic attacks, including both bosses! Resistance is generally seen as the best way to take down tough enemies, so check out which classes and gods can give you access to it.
2. Don't be too afraid to blow some resources right off the bat to get some early high level kills. But by the same token...
3. Don't waste too many resources levelling later. A good time to start fighting the Indomitable is level 6. When I'm playing Naga City, I tend to go down to the boss floor just before i get to level 8.
4. Specifically for VHoS - There are quite a few ways to take off more than one death protection per attack: Knockback, Mana Shield (Sorceror Class Trait), and discharging burning will all wear the Indomitable down quickly. Prep a burn salve for his corrosion. Also, blahblah *is* the tougher boss - you need to fight him with the map fully revealed, he does tons of damage, and has a *lot* of HP. Save resources for this guy!
5. Specifically for Naga City - The dungeon is all about building a crazy strong character, so long term bonuses really shine. Pick a race that gives good long term bonuses (Human, Elf, Dwarf). Alchemists scroll is awesome. If you don't pick up magic resistance, be careful about the fight against Kinisssch (He's a little tougher than he looks). A nice little tip I found - If you have some knockback damage, you can push super meat man into any other boss and basically get two kills (This is a fantastic way to get past the tower of goo).
Essentially the other half of Naga city is knowing your gods. You can prep a single god on the upper floor (Personal preferance: Binlor). Once you're at the boss room, you have access to all of them. Half of Naga city is figuring out how to extraxt maximum efficiency from these guys - which gods to worship, when to use consesus, which gods to desecrate and, of course, which boons to take are all factors.