Although I'm not exactly sure what they're talking about in that passage, the word count there is just what it's supposed to be—the verb count. There is nothing special about it. It means being important or significant. In other words, it has the same meaning as in the following example:

What counts the most when applying for a job position is work experience. The more work experience you have, the better chance you've got to get the job you want!

that blip in time simply means a very short period of time. More precisely, that blip in time refers to that less-than-a-second period of time they're talking about at the beginning of the sentence. Here's a step-by-step breakdown of that last group of words that you don't understand:

you better make [that blip in time] count
you better make it count
you better make it matter
you better make full use of it

Although I'm not exactly sure what they're talking about in that passage, the word count there is just what it's supposed to be—the verb count. There is nothing special about it. It means being important or significant. In other words, it has the same meaning as in the following example:

What counts the most when applying for a job position is work experience. The more work experience you've got, the better chance you have at getting the job you want!

that blip in time simply means a very short period of time. More precisely, that blip in time refers to that less-than-a-second period of time they're talking about at the beginning of the sentence. Here's a step-by-step breakdown of that last group of words that you don't understand:

you better make [that blip in time] count because it's too short
you better make it count because it's too short
you better make it matter because it's too short
you better make full use of it because it's too short