I recently did a split stay at Poly and BC where we had dining plans at both resorts.
The way I did it was to book ticketless annual passholder + dining packages at both resorts (if the lead guest on a reservation is an annual pass holder, then you don't need to purchase at least one day of park tickets for every person on the reservation at each resort).
Later, when annual pass discounts came out, I applied those to our existing reservations (these were, in essence, an additional 5% discount over the general public discounts offered over the same period and the resulting savings difference was roughly equal to the cost of upgrading one MYW ticket to an annual pass).
After that, I bought everyone's park tickets (to cover our stay at both resorts) at a discount from
Undercover Tourist.
All of the above purchases (as well as our air fare) were done on my Disney Rewards Visa (right before heading to WDW, I transfered all of the points to the Rewards Redemption Card).
Once at WDW, I then attempted to upgrade my ticket to an annual pass by price bridging it first (to get credit for the current gate price) and then using my Disney Rewards Redemption Card to pay most of the difference (this is the one area where I had a headache as the CM overcharged me for the upgrade - there's a whole thread on these boards about that saga, which was ultimately resolved after I returned home).
In short, aside from the price bridging headache (which, I suppose could have been avoided had I just bought the tickets directly from Disney), it worked out great.