First of all, if you run out of cotters, let me know what diameter and/or the make/model of crank, I can probably help. I have a wide assortment of NOS stuff, but
not because people PM'ed them to me as I've requested above my avatar for years. People be stingy with them cotters!
That said, proper removal, proper fitment should be done with a legit cantilever/bypass press like the VAR07. There's a trick to using a VAR07, and it seems not many these days are familiar with the tool Go figure! There's an adjustment to be made using the bolt coming out of the top of the tool on same side as the short arm. The biggest mistakes I find newbies making include 1) Hyper-adjusting the tool's jaw adjustment bolt so the tool clamps too hard too fast, which bends or mushrooms the cotter leaving the threads toast or leaving you drilling out the remnants, or 2) Not getting the jaws square over the cotter before clamping, which also often leads to bending the threaded side, or 3) They don't have the open end of the jaw over the blunt end of the cotter, so it's pressing the cotter in, not out
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My advice to newbies is this. Get a VAR07 or find someone with one. Spin the adjustment bolt out significantly. Clamp the jaws correctly over the cotter loosely. Spin the adjustment bolt on the VAR07 down until the jaws make contact firmly with the cotter, where the split side of the jaw is making clean contact with the crank arm, and the press end is firmly on the threaded end. Now it's tight but not yet tight enough to press the cotter out, take the VAR07 off the crank, spin the adjustment bolt 360º to close the jaw a little more. Now try to press out your cotter with the VAR07 perpendicular to the crankarm, so it's nicely square over the cotter. If you're still not able to press it out, pop off the VAR07 again, spin the adjustment bolt down 180º to tighten a little more, then try to press out again. Repeat 180º tightening of the jaw until you press out. By going light and working up to a firmer jaw stance, you'll have a better chance of pushing the cotter out, potentially in a condition where it can be re-used. This is what I tell newbies to do so they don't make a mess of things. You start to get a feel for what's right with time and experience, the reality is you only need half an inch of actual movement to generate the force required for cotter removal, so you DO NOT want the arms of the VAR07 to be really wide-open. With the arms of the VAR07 wide open, you're going to work 10x as hard to close the arms. Use your simple machine, leverage, to do the work for you!
Proper fitment is also a process. In my opinion, this process involves pressing in and pressing out the cotter multiple times. Press your cotter in until it stops. Pop it back out. Look where exactly on the wedged face it's making contact to know where to file the face of the wedge so the cotter fits nicely in. I have a proper cotter vice, but I used to use the magnetic rubber covers back in the day to hold the cotter in a bench vice so I'm filing the face perfectly straight.. I've seen guys who can just take a cotter in their hands and run it down the file, and I met one guy who used a disc sander! After filing the face, press in again. If it's not quite in the correct depth, pop it out again, look at your mark where it bottomed out, repeat filing the face. I normally aim to press mine in so only 3mm-5mm(ish) of the blunt end is exposed after fully pressing in.
BTW, the face marking method [MENTION=57649]iab[/MENTION] describe is excellent, especially if you don't do it often, or your eyes are going to hell like mine, it's almost like using a guide coat with body work, or marking blue for metal work. Black sharpie works fine.
When I'm doing my final press, I'll sometimes give the VAR07 adjustment bolt another quarter or half turn to really press it in there. Again, you don't need much!
Top it off by installing the washer and cap nut, then tightening fully. NEVER use the dome nut to "pull" the cotter into place. If you were able to generate the force required, you'll probably strip the threads first, making your cotter worthless. I know, there are people who will swear they've been able to do this, but if it's a new cotter, chances are it'll wiggle out with some riding.
Just be careful, don't over-file. You can't add metal back.