I can't really help with AP because I have never ordered from them. I have heard sometimes it is better or easier to use a shopping service to buy items from them because the English store stock is very small and not that great of a selection.
For Baby, there is information about ordering on this page:
<-- shopping cart tutorial, pretty Engrish-y but straightforward.
The shopping cart system is basically like any other site, all fields marked with a red asterisk are required. You shouldn't have to bother with the other information as it only applies to Japan residents.
After you place your order, you will get an automatic confirmation. Later you will get the real invoice (in English) with total cost with shipping, and info for Baby's paypal account where you must
send your payment in yen within seven days (failure to make payment in time can result in blacklisting).
Once you make your paypal payment send them an email letting them know you paid. Once they confirm that the payment has been received they will send your items.
edit: oh yeah, and about sizes... Yes, most things come in one size (which is supposed to be Japanese M but it also depends on the cut of the individual piece). Baby makes a few items like blouses and some dresses in S, M, and L sizing. Specific measurements for each garment (garment size, not body size) should be listed on the product info page... make sure it will fit before you buy it.