I do this on most all of my knives that have holes predrilled for tip up or tip down carry. Only diff between me and you is that I like the clip and use it in a tip up carry mode. I then fill the other holes with custom made screws.
Just did my Spyderco Veile folder this evening. First find out from the Spyderco Golden Col plant what the size of the screw is on the Manix and get some from a knife supplier. If you can't do that you can maybe use the three existing screws for the clip to find out or compare to others. A bag of 50 button head screws will run you about 5 to 7 bucks depending on where you buy them.
You will also have to go to Sears or Lowes and get some cut off discs for a dremel. Then put them on a handpiece and cut off the excess after mounting the screws on the handle on the inside of the tip up carry slots of the knife so they are the right length and so they don't stick out and you have plugs to fit right in the holes. Button head screws work best from my experince and torx are better than phillips or hex head.
Just get the bigger diameter cut offs so it can reach down into the knife body and cut off the excess part of the screw that sticks out on the insideof the handle. The reason you use the tip up carry slots is because you have easy access to the excess from there. Just do one at a time and after you cut off the excess unscrew it and do another until all six are done. You will scratch up the inside of the handles a bit but just take your time and then you can smooth that all out after finishing off the last one..If you knew the size and had the tap to thread a piece of brass or thin metal you could use that to cut the screws down and not scratch up anything at all on the knife.
If you know you are keeping the knife and that you don't intend to use the clip ever, you can cut off the excess of the three screws that come with the knife and use them to start.
Most screws for pocket clips seem to be a 2-56 size these days but I noticed on the Spyderco Viele folder that I bought recently that the ones in it are bigger than that. Because the knife you have or rather, the knife you are getting is made in America I suspect you can find the screws that are in it. My Endura by Spyderco looks to have 2-56 screws but they are not that size. They are actually just a hair smaller in diameter than the 2-56 I have. What ever the screws in the Japanese Spydercos are they are probably metric and perhaps even unique to Japan and/or China and Taiwan. They may not be available here from knife supply houses. I just happened to have some that fit my Viele but I could not tell you the size they are. Found them lose in my spare parts jar from old knives I've taken apart.
This is another option. You may be able to buy a cheap Chinese made knife for just a few bucks that has the same size screws as your knife and use them to fill the holes. For example Wal-Mart sells that cheapy Winchester knife for five to six bucks but if you look around you can probably find some at Smokey Mountain Knife works or some other place in a grab bag for that or less.
You could always plug it with glue but if you want it to look good I don't think you can do better than some button head screws in a torx or hex head.
