ah, I'd rethink this idea. If you have blockage, that's your real problem to solve. Keeping the correct levels between ponds is critical as you don't want to overflow the top and lose water that way (unless top pond is OVER lower pond) nor do you want to overflow the bottom pond with too much from the top. Also, if you have a power outage, you don't want the top to overflow the bottom as it empties (which is the other problem). This is the danger I see with drilling holes in the top.
I'd make sure you have ample area for the top to pour down into the bottom so no debris GETS stuck in the first place. Either figure out a screening system to allow water through but block debris or let the debris fall into the bottom pond where you can manually or via filter, take it out.
My similar setup would be my bog (raised body of water) flowing into my pond (lower body of water). When I get a power outage, the water in the bog will stop flowing once it reaches the bottom of my 'weir' lip. No water lost. The pond gets minimal additional water as the level of the bog water is about 1" above the weir. Any debris in the bog falls into the pond, so no blockage that way. What happens with this type setu though is the water in the bog can rise and yet the same outpour happens. Thing is, my bog walls are 6" higher than the bog water level, so it would take a huge blockage of the weir front to start water pouring over my bog walls. Your upper pond probably does not have this saftety factor but you could consider this idea. The main reason you probably don't do this is because it doesn't look as nice to expose so much upper wall plastic. There's ways to cover this but since your upper pond should be basically ALL water, this should not be an issue, unless of course you have the problem you outlined above. Make your 'pouring' part from upper to lower wide/deep/long enough to get a lot more water through IF IT BECOMES necessary via blockage.
Others more experienced with two tier ponds hopefully will chime in and correct me if I'm wrong but I'd surely not do as planned. And using preforms are a problem waiting to happen, be it by cracking in short time or becomming out of level through frost and thaw cycles. Just be aware. In the future, consider a liner (hdrpe or epdm) and you'll have a lot more peace of mind.
Good Luck!