It depends where you have them and whats around them. I fyou leave it stock and jam them in there then yes you risk big overheating. Especially if you have a big box setting on them. If you make a false floor and take the foamies out then there could be enough flow to handle cooling them.
That should be ok. You just want to leave a hole up to the side of the trunk behind the fake covers for the taillights(theres about a six inch distance between the two). This opens you up to flow throughout the car. Just monitor the temp and if you need to put a fan on the side and keep the air flowing through the trunk and car do that.