What is the best way to align them? I will be doing this in a couple days so it would be very helpful to know.
1) Put the gas block on the barrel upside down (but with the back towards the back) and determine how the gas port in the gas block interfaces with the gas port on the barrel. On many/most gas blocks, room was left for a conventional handguard cap, so without that cap you will need to leave a gap between the gas block and the shoulder on the barrel to get perfect fore/aft alignment. On some gas blocks (noted above) no room was left and you just push the gas block against the barrel shoulder. Note any gap you need - a feeler gauge measurement would be ideal, but you can probably eyeball it and be fine, the port on the block is usually much larger than the port on the barrel (unless you have a 300BLK barrel, or something funny like a 16" with rifle length gas).
2) Put the barrel in your upper with the pin in place at the nut area, and confirm that the gas port is pointing perfectly vertical. It should be, and will on any decent barrel.
3) Install the barrel in your upper per whatever directions.
4) Install the gas tube into the block before assembling it onto the barrel - not required, but will usually make things easier.
5) Install the gas block onto the barrel. Align it perfectly vertical based on eyeball, straight edge use, or fancy tools if you're a machinist. If it's not a sight base, the vertical alignment only needs to be good enough for the gas block port to fully cover the barrel port, and again, the barrel port is usually much smaller than the block port. Align the gas block fore/aft based on whatever gap, or no gap, is needed per step #1. Again, a feeler gauge measurement would be ideal if there is a gap required.
6) Tighten the gas block clamps. On non-serious-use ARs I have not used any locking chemicals and haven't had any problems. For a serious-use assembly I would probably want to use Rockset, since it's highly heat resistant but also removable without destroying anything. Blue or purple Loctite weakens at gas block temperatures, and red Loctite makes disassembly a pain, at best.