I would like to answer your actual questions but I'm afraid I too get a little confused with the choice of primary vs extended partitions. I also prefer to partition my hard drive if it is large. I feel it helps me find things easier.
I usually just select primary partition for each and I've not had any trouble. If you create extended partition then I think you must also create logical partitions inside of it.
Hopefully someone with more knowledge than me will come along and try to answer your questions.