The alternator supplies all of the power to all of the electrical accessories (amplifiers, lights, power windows, power seats...) as long as the engine is running. Upgrading the alternator is generally the most cost effective way to add more performance to your system. In the next few paragraphs I'll attempt to explain why other remedies may not solve your problem and may even make it worse.
Many people want to know when they should replace their alternator. The short answer is... when it fails. If you just want the battery to remain charged and your present alternator is keeping it charged, it's doing its job. If you want a system to be as close to perfect as possible and money is no object, replace your alternator when you install the amplifiers.
Extra batteries are great if you want to listen to your system with the engine off. While the alternator is charging, the extra batteries will only draw current which could otherwise be going to your amplifiers. For proof, all you have to do is measure the voltage while the engine is running. It should be approximately 13.5-14.4 volts DC. Then turn the engine off and measure the battery voltage again. Now it'll be around 12-12.5 volts. Whenever the voltage at the battery is up around 14 volts, there is current flowing into the battery.
One Farad capacitors:
Large, one Farad, capacitors only help to maintain the charging voltage for a tiny fraction of a second under high current demand situations. They do a fine job of filling small dips in voltage and may help reduce your lights from dimming but they won't really solve your current supply problems if your alternator can't keep up.
NOTE: Capacitors DO NOT increase the charging system's voltage.
Battery isolators only prevent draining your starting battery when playing your system with the engine off. Most of the time they will actually rob power from your system. Diode type isolators will usually have a small voltage drop across the diodes (approximately .4 - .7 volts). This loss of voltage will dissipate power in the form of heat and unless you're freezing to death, it doesn't help matters. Solenoid type isolators don't have as much voltage loss as the diode based isolators but the solenoid coil does pull current. Some coils may pull as much as 3 amps of current. Now 3 amps of current isn't much but if you're using 2 solenoids and you're already having trouble with a weak alternator, it'll just add to your problem.
... now, all that being said - I have a 500 watt (rms) system with 2 amplifiers and the alt just barely keeps up. Under extreme
loads voltage can drop slightly under 12 with a very small amount of headlight dim so I can't imagine an 800 watt system would be too much worse but you be the judge. You're correct with regard to the alternator - it's not very powerful and in addition, it's too noisy for competition or audiophile standards (honda alts are notorious for this).
If you have the money, I'd suggest upgrading to a high output alt of better quality especially if you wil go above 800 watts rms.