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TL;DR: How do I properly combine a battery charger and a battery step-up switching power supply into a robust power delivery circuit?

I'm building my first AVR-based portable device (yay!)
It will drive some LED counters, which are a little bit power hungry (boo!)
It needs to run for a day at a time (argh!)
I'm thinking it will draw on average about 100 mA at 5V. This means I'd want something like a 2200 mAh 3.7V Li-Ion cell to power it, for enough energy, and a boost-type switching controller for going to 5V and being reasonably efficient with that energy.
As an additional requirement, I'd like the device to be chargeable by simply plugging in a wall wart. However, I haven't designed any chargers before, so I'm hoping to look before I leap by asking the advice of this august collection of contributors!

The circuit will be something like:
[Wall Wart ->] Linear charging regulator -> Battery -> MC34063 switching regulator -> Arduino/AVR
I can put a rectifier diode from the linear regulator to the battery, so the battery doesn't power it backwards when un-attached.
Also, I have an analog-in left on the AVR, which I can use as voltage sense (or current sense?) for controlling the charging, even though the Li-Ion cell already has overcharge/overdischarge protection. Something like a depletion-mode MOSFET between the charging regulator and the battery will let me control the charge, while not getting in the catch-22 of having to power on the AVR to allow it to charge, but not having enough charge to power it on, which I'd be into if I used an enhancement-mode switch :-)

Things I especially worry about:
# Wall Wart + 5V regulator + 4.5 ohm depletion mode MOSFET -> battery -- will this be sufficient for charge control? I think so, but I've been wrong before :-)
# Charger -> Battery -> MC34063 step-up regulator -- when charging, I'll get something close to 5V on the input, which is also what I will set the output to. Will I drive the regulator bonkers here or will it deal with it? I'm using the step-up circuit from the data sheet (see attached -- I adjust it to go from 3.7V to 5V instead of 12 to 28).
# Mechanical connection of the battery -- any good, solid components that add zero weight yet can take a crowbar to them and keep sticking? Recommendations solicited :-)

I'll listen to and appreciate any and all advice!