Making a schedule

OR

Making a schedule is not easy, but it is very helpful to achieve goals.

OR

Making a schedule is not easy. However, it is very helpful to achieve goals.

The "while" clause has to come first. The contrasting clause follows.

"while" functions as "even though"

Ex. While you turned out to be a great kid, I still wish I had given you up for adoption.

Ex. While Sunshine Ranch is an excellent place to go [horseback] riding, I'm thinking of going somewhere else because their rates are very high.

Whether you can complete your goals on time or not depends on how you use your time. Perfect

And spending your time scientifically means you have to make a schedule.

"scientifically" was misspelled (I don't blame you). However, it's not the right word anyway.

The word you want is "efficiently".
 
I have a full schedule for these next two months.

I think this is what you meant :)

You could say "these" or "the".

I don't know if I can run on my schedule.

This sentence is okay and makes sense, but it sounds a little strange to me.

I think maybe you are trying to take from "to be running on schedule" or "to run on schedule", which refers to being on time.

There's some different variations that would work too, such as:

follow my schedule

keep to my schedule

stick to my schedule

adhere to my schedule

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Great job!

I have definitely improved my schedule-making skills over the past several months, but I still need to work on my schedule-following skills :P :)

Making a schedule