You can configure your packages now for pro-rata, if they purchased a 1 year term then it would be prorated to June 1st or July 1st depending on what you set for the cutofff day. Then you can adjust the renew date and generate a 2nd invoice for June 1st - Jan 1st. After that it'll renew on Jan 1st each year. So, an extra manual step in there unfortunately. We might be interested in adding a prorata month option for yearly services if you want to make a feature request.
Prorata option works best with monthly services, so if you have a monthly service you want to renew on the 1st each month, then placing an order will prorate it.. and you pay either partial month or partial month + whole month to get it to renew on the 1st. It doesn't work so well with yearly terms because it will still prorate it to the 1st of the next month not the 1st of a particular month.