No problem. I've had situations where a card had a credit limit which wasn't high enough to let me use it as I wanted through the month, and, by making partial payments, was able to take better advantage of a rewards offer.
The reason you suggest, solely for utilization purposes - keep in mind 2 things. First, the issuer only reports the balance once per month. As of now (2019) I haven't heard of a card that reported multiple times during a cycle. Of course, if we hear of one such bank...
The other thing, until a couple years back, the advice here was based on the card reporting a balance as calculated for the bill cut each month. I went along with that since I had no evidence to the contrary. Then I noticed my score drop. When I reviewed the details (you can use on line services such as Credit Sesame, Credit Karma, etc.) I saw that a card I had, in fact my 'main' card, started reporting at month end, not the bill balance. To be clear, I was in the habit of paying my card a day before the bill was cut. So the reported balance was close to zero. The card billed on the 15th of each month. I found they started reporting the balance on the 30th/31st, i.e. the last day of the calendar month. This prompted me to pay, not just the card statement balance, but to look and pay the charges since that time until the end of the month.
In the end, you seem to be more in the first category, where you have a low card limit. Using it, and making multiple payments is fine, and might prompt the lender to raise your limit. If you are focused only on your score, keep in mind that utilization has no memory, I can use my card as normal, but if I need to maximize my score, go back to pre-paying the card and once the zero utilization is reported, gain back the lost points.