So how do you factor FPM
With .003 - .006 gear setting?
Am I doing this right or is there another way?
1000 rpm x .003” = 3” a minute ?
You are correct that with those two settings, the carriage will travel at 3 inches per minute, but that's not what you're after. You don't care about that number in this context. The only number you care about there is the is the actual feed number. 0.003 or 0.006. These do not (on a lathe) get figured into feet per minute. They are based on a geared relationship, so at 10 RPM or 10,000 RPM, every time the spindle rotates one time, that's exactly how far the carriage will advance.
FPM, SFM, SFPM, depending where you read it, is surface feet per minute. That is based on the selected spindle speed, the How fast the work surface rotates past the cutter. This number you have to calculate, as it is related to the diameter of your work.
There is no chart that correlates these, because they are totally separate settings. You set the surface feet per minute by adjusting the machine's RPM, or spindle speed. That's based on the cutter and the material (And some practical experimentation... They're a guide, not a rule).
Setting the feed rate, the 0.003 and 0.006 numbers totally separately, based on horsepower, depth of cut, desired finish, tool type, etc. and does not change at all as you adjust the RPM for changing diameters.