Both of your Caps should not be needed, if you are going to install a second battery in the trunk to run your system off of. This along with an upgraded Altenator should be more than enough juice.
Also a very important upgrade for stereos is the Big 3. This is always the weakest link.
The reason caps are used is because they can provide instant power, at the second its needed, like when a heavy bass note hits and your lights start to dim. A battery on the other hand can not provide power as quickly.
While caps do have a purpose alot of people assume that it is going to fix this problem.
If used with the Big 3 upgrade it can help.
I would see if you can return one of the Caps to get your money back as you won't be needing both.
The problem you are talking about with charging your caps is probably due to either the incorrect resistor size or the resistor getting too hot.
I never really have any problems charging caps, just do Not try to charge it for longer than 2 minutes max or the resistor will get really hot and not allow much current to flow.
The reason you charge the Cap with a resistor before connecting it, is so that there isn't a massive spark that blows the inline fuse or damages the cap.
You should only need to charge the caps once before installing. As long as they are close to 12 v it doen't have to be dead on.
I would try upgrading the Big 3 first, before spending money on batteries, a new Alt and before installing the caps.
You may be able to get away with one cap + the Big 3 upgrade.
92 Bonneville SSEi - Stock - Remaining repairs needed due to neglect by previous owner - ABS/Trac, AC.
Mods so far: Maganflow High flow Cat, Rebuilt */C
Future Mods: Interior swap for Leath, High Output Altenator, Crazy system, Climate Control swap & Custom Exhaust/Intake.
98 Dodge Stratus - Wifes Daily Driver
92 Dodge Shadow - My Winter Beater