Can I use Perma-Chink or Energy Seal for my checks since I have some left over ?
You may but there is also a product specifically designed for filling cracks (or checks). Homeowners often want a contrast with texture and color when using chinking, but usually want the checks in the logs to blend in a little more. When filling checks, particularly on wide ones stuff some soft foam backing rod 3/8 below the surface of the logs, then fill and smooth out. It doesnt hurt to pour in some Shell-Guard first. If your checks have been exposed to the weather, chances are some water has gotten in and the possibility exists some rot may be growing. Shell-Guard will help kill the rot and help prevent it from getting any worse.