The FCC has put out a statement that it is illeagle to use any amplifier with 802.11 products unless the amplifier and the system have passed the FCC testing as a unit. This is why Linksys can sell an amplifier, and others like Wave Wireless can sell one. But most of the amplifiers being sold are by independant companies who do not make access points. These companies usually say the product must be used in accordance with the law. It is up to you to know the laws, and apply them properly.
The FCC also came out with a statement that says that an installer can no longer certify that a 802.11 system complies with the part 15 rules. The entire system bust be previously tested by the manufacturer and approved by the FCC. If you use an amplifier, you are in violation of the rules and may face stiff penaltiies from the FCC.
Be also aware that there are licensed users of this spectrum. Your manual clearly states that you may not cause interference to them. In Dallas, the FCC shut down an apartment complex WLAN because it interfered with the licensed users.
You should design the system to work without the amplifiers. With the proper antennas, you should never need them. This also reduces this unwanted interference.
The answer to your technical question is to do all the calculations in dB and just add or subtract the numbers. For example AP @ 100mw = 20dB, antenna gain 3dB, coax loss -3dB total 20dB.
