Arranging disks and partitions is always a bit tricky to advise on since if you ask 2 different persons you will probably get 2 different answers but in your case you can think about 3 basic scenarios:
Wont make you coffee and eggs in the morning but putting the 2 disks on a RAID0 setup will give you a significant speed boost, looks very attractive an you can just partition the disks as you like like you said on your question;
Have in one of the disks the 2 operative systems installed and use the 2nd disk as a share between Ubuntu and Windows to keep your personal files and backups. Disks that have less access tend to break down less (this is not a universal rule but tends to be true);
EXTRA safe setup:
Create a RAID1 setup where all you data will be stored equally on the 2 disks, if one fails the other will contain all you hard working projects and personal files;
Easy split setup:
Use one disk to install Windows and the other to install Ubuntu. Keeps your systems apart, gives you some security over the stability of your systems (if you break down Ubuntu or windows it wont interfere with the other and can be easy fixed by repairing the MBR) and when you get tired of using Windows and you finally decide to use only Ubuntu you can just erase it and use the 2nd disk for your backups and files ;)
Just pick one and go with it, if you have 2nd thoughts later on (you probably will!) you can just choose another and test it up. Personally I always go for safety but I don't like wasted space so I would choose the safe setup: keeps my data on a 2nd disk, allows me to share date between systems very easily.