Afaik this is not possible with the New-VM cmdlet, you will have to use the CloneVM method.
There you can specify where each individual harddisk should be created.
Blog: lucd.info Twitter: @LucD22 Co-author PowerCLI Reference
You can probably have the template with only one disk (OS-disk) and specify where that should be, and then after add the second disk. Something like:
$Template = Get-Template -Name "tmplate"
$datastore1 = get-datastore ds1
$datastore2 = get-datastore ds2
New-VM -Template $Template -Name vm1 -Datastore $datastore1
$vm = get-vm vm1
$CapacityGB = 15
$vm | New-HardDisk -CapacityGB $CapacityGB -Datastore $datastore2
Obviously this can be done more effectively, but that's depending on what you want to do with the script. If you for example want to deploy multiple VM's through the script, then I wouldn't recommend using a static VM name like i did here (vm1).