You have now interleaved the peg plans with the results appearing in the first design.
Another way to do this is to create a threading, and then just draw your design underneath it. WeaveMaker will figure out the pegplan for your design (or the tie-up, if you are in treadling mode.
The first pick is at the bottom because that is how a fabric looks as it comes off the loom. Imagine that you are sitting at the loom. The first pick you weave is closest to you. If you have a draft (on paper) sitting alongside the fabric, you want the draft to look just like what you are weaving, which requires the first pick to be at the bottom of the piece of paper. There is no sensible reason to draw drafts upside-down, although some handweaving books mistakenly do it that way.
The location of the first end on the left is arbitrary (it could as well be on the right), but mills all put it on the left, so that is how WeaveMaker does it.
The question of "ports" on modern computers is complicated. The explanation here is written somewhat from the perspective of WeaveMaker and Macintoshes, but it's increasingly the same for Windows computers.
Older computers (both Mac and Windows) came with built-in serial ports. On the Mac there were two, usually called "modem" and "printer". Similarly, Windows computers almost always had a serial port, called COM1 (and if there were multiple such ports, the others were COM2, COM3, et cetera).
The problem with these older serial ports is that their design literally pre-dated computers. They were engineered back in the days of real Teletypes, the kind that were used to send real telegrams, delivered by a person weaving a uniform, complete with hat. These older serial ports were slow, and the way they worked wasn't compatible with modern computer electronics, and so they required expensive chips inside the computer to accomodate them.
To solve this problem, the Universal Serial Bus (USB) port was created. (Confusingly, this name contains the word "serial", which is also used to describe the older ports. Sorry, I wasn't responsible for naming these things!). USB is fast, completely compatible with modern computer electronics, and is therefore relatively inexpensive. USB is great for hooking up printers, extra disk drives, cameras, scanners, fax machines, music keyboards--it really is universal. So that's good.
Problem is, all the computer dobby boxes on the market today were engineered to use the older, slower serial ports. To get a modern computer to talk to a dobby box, you need a USB-to-serial adaptor. This lets a USB port act like the older serial ports.
Now, this creates all kinds of headaches for weaving software:
1) It used to be that the software could count on the computer having at least one serial port. Guaranteed. This is no longer true. If you don't have a USB-to-serial adaptor, then your computer has ZERO serial ports.
2) Merely plugging in a USB-to-serial adaptor isn't enough. There is almost always a piece of software you also have to install. It's often called a "driver", and without it, your computer doesn't know what to do with the USB-to-serial adaptor.
3) Even after you get your USB-to-serial adaptor set up and working, nothing stops you from unplugging it, at which point you still have the software driver installed, but you no longer really have a port, because the hardware piece of it has been unplugged. This situation may look different to the software than if you had never installed the driver (depends on the way the driver software was written).
4) There are other ways to put an old-style serial port on a computer. For example, you could do this with a Bluetooth adaptor. So your weaving software has to look beyond merely USB-to-serial adaptors.
5) The list of "dobby ports" that displays on one computer may be totally different from what appears on some other computer, and yet both may be perfectly fine and correct.
So what's the bottom line? Modern weaving software has to do the best it can to examine your computer and find your USB-to-serial driver and associated hardware. And as I've indicated, there are many ways to do this, and many ways in which it can go wrong. The software then has to issue error messages as appropriate, to try to help you resolve the problem. This is not easy!!!
If you are having trouble with your serial ports for dobby weaving, consider: is your USB-to-serial adaptor plugged in, and is your software driver installed? That's the starting point. If your "dobby ports" menu is blank, one or the other is presumably missing. Don't rely too much of what other people see if their "dobby ports" menu, because it's likely different from what you should be seeing. If you need to write to us, what brand of USB-to-serial adaptor do you have, and what model number is it?