How do I get the battery markings on the bottom of the board?
If you flip the battery holder then it should go to the bottom of the board (either flip tool or middle button/scroll wheel when moving the part)
One of those chips is extremely fine pitch.
I use a hot air gun to solder these (the FTDI is the finest I've done so far), easy, just run two beads of paste along the pads and hit it with the hot air. Clean any bridges with solder wick.
I have soldered 2 DS3231s with a 2mm chisel tip soldering iron (no extra flux) as well 16 dual colour 0805 LEDs and those tiny SMD 0.1uF caps and some other stuff - just takes practice. I did lose a capacitor in my solder when I got distracted though :D Oh - smallest I've done are some of those SMD resistor networks with 8 resistors in each in a package about 3mm long.
.. the 1284p is a low power device with <<1uA power save and power down.. Did you think on switching off the various chips on the board when they are not accessed? E.g. via a transistor in their Vcc.. Otherwise they can take ~mAmps.. A green board design..
Hmm. Interesting idea but I don't really have any knowledge of low power stuff so have no idea :D