I have never completed a civ 4 game, and the furthest I have got are in pbems, so I'm supposed to be learning as I go, but really I feel like I'm flying blind.

I have one game where my capital fat cross is 9 or 10 river flood plains, 2 gold bearing hills, and some hills with forests, and a couple of plains.

With the flood plains, do I just build cottages on them, becasue 3 food is plenty, or should I irrigate some?

Any suggestions for optimal development... 1.61.

you should count you food needs:
+2 food from city center
+1 food from flood plains
-1 from plains
-2 from plains hills

with that, you know how much food surplus you have at size 20
If it's positive, you need no farms.
If it's negative you would need as many farms as food lacking.
If you have that much flood plains, you're certainly going to have health issues. Settle on the river, keep the forests.