I have a minibow 2.5 that I keep my Betta in. It came with a tetra microfilter it's a HOB deal. Anyway I am using it, but I don't have it filled all the way up, it's about 3/4 of an inch or so from the top. It seems tofilter the water better and my betta is doing fine with the water level. I asking people with a similar setup is it ok to keep the water level like this or should I just fill it up or does it not matter.

I have one and keep it filled up. It creates less current and gives the betta more room to swim around.

You are not filtering the water any better by keeping it less filled. If I am correct, the minibow is a regular in-tank filter. You may be kicking up more particles that get filtered, but a cycled filter will do much better even in a tank that small.

As already stated, that added current by filling the tank less than normal is far from ideal for a Betta. Fill it up more and let the current disperse over the surface. That is a much better approach.
Also consider getting an appropriate sized heater for the tank.