(The bulk of this answer concerns paper miniatures that stand up on the battlemap. For information regarding tokens that lie flat on the battlemap, see Addendum 2 below.)
It's difficult (and not really necessary) for paper miniatures to be the same scale as the map. You can approach this in many different ways, but the solution you choose has to be based on what looks good to you, because there isn't really a correct way to make paper minis.
Here are a couple of my own illustrations as examples: A lizardfolk greaser and his slavering wolf companion.
They're basically to scale with each other, right? Sure they are.
The typical scale for tabletop battlemaps is one table inch to five D&D feet. Assuming that's what you're doing, I'll be treating a square in my image editor as "one square inch" in paper terms. From your question, I get the impression that the minis you made look sort of like this:
The humanoid figure takes up most of the width of the square, and looks great, but the wolf has to be squeezed to fit in, and it does not look great.
Of course, if the lizardfolk is about one inch wide and over two inches tall, and we take the figure to be to scale with the surrounding map, that means he's over ten feet tall, which is not what I had in mind. To make these tokens be (more or less) in proportion with the five-foot grid, we can do something like this:
The lizardfolk is just over an inch tall, which means he's "really" about 5'9", which is what I was going for. The wolf appears to be five feet long and two and a half feet tall. When these guys are placed on a battlemap, your table will look like a real dungeon with a real lizardfolk and a real wolf that all got shrunk down to 1/60 scale. That may be exactly what you want!
...But for my money, they're both too small. (The squares in these images are probably not one-inch squares on your display, so look at a ruler to see what I mean.) I prefer for my handmade minis to be bigger, so they're more visible and easier to pick up (and so my players can better admire my unparalleled artistic talent). When I printed out this lizardfolk recently, I made him a little over two inches tall, as seen in image #2 above—it didn't bother me or any of my players that he was grossly out of scale with the surrounding battlemap. That kind of abstraction is totally allowed.
The "wideness" of the wolf is still a problem, though. If you print it out at the scale I picked for the lizardfolk, it's definitely too big. It takes up two squares on the map, which a Medium-sized wolf is not supposed to do:
If we're sticking to one-inch squares, then it's going to be tough to determine what space this wolf is occupying.
Here's a compromise that I rather like:
The wolf is spilling out of its square a little bit, but that's manageable. The lizardfolk is "technically" about seven feet tall, but I don't mind. What's important to me is:
- All the minis are big enough to see and manipulate without difficulty.
- It's clear where each creature is, making it possible for everyone at the table to play tactically.
- The characters are to scale with each other, giving my players a clear idea of how big things are supposed to be, even if they're not to scale with the environment.
Addendum 1: Printing Out Standing Miniatures
(This may go beyond the scope of the question, but I hope it makes my answer more clear.) Regardless of the scale you choose, you can print out your minis in a few different ways. Here's how I do it. In my image editor, I put two copies of the image together, one flipped 180 degrees so they meet at the head (with a bit of space in between).
I make sure the grid really is one inch squares, and then I print this out on cardstock. The dotted line indicates how I cut the guy out, leaving about 3/4" at each lizardfolk's feet.
Then I fold between the heads, I fold below their feet, and I glue the two bottoms together, like this:
You could also fold the "bottoms" out and glue the backs of the two images together, creating a ⊥ shape. If I did that, I'd probably glue a square of cardboard to the bottom to make it sturdier.
Addendum 2: Tokens that Lie Flat
I don't think any of the above solutions work if your character-representatives are going to lie flat on the battlemap. Any character who's big enough to see is going to be too big for its square—and everyone looks like they're lying on the dungeon floor. This is probably a matter of personal preference, but I don't like the idea at all!
What I'd do instead is use only the characters' portraits for tokens, maybe with some borders. Maybe something like this:
I could print these out, glue them to some cardboard, and cut them out really fast. They'd be easy enough to see and manipulate, and I wouldn't have to worry about scale at all. They'd travel well, too: I could toss them in a dice bag and not worry about their being bent or torn. (Also, I'd only have to draw the characters' heads, which would have saved me a few minutes.)