Run boundary is a test to determine if anything is in the path of the endmill bit. I would suggest that you do not run boundary just above or right next to the workpiece. Set the height (by jogging the tool) some 20mm clear of your workpiece plus make sure your jog height has accounted for the clamps in use. That way the run boundary command will not push the tool bit into anything while the command is running your machine. The command will let you see in a practical manner where any potential obstructions are going to foul the tool bit at any point in your toolpaths that are a part of the job you wish to accomplish.
I do it somewhat differently and have no need to run boundaries in CNC work. I created some clamps and a table that uses them so that the height of the tool bit when it is moving without cutting, cannot foul the clamp height. I also made the clamps so that the clamping area could not be fouled by the tool bit. My clamps do not intrude on the workpiece more than 5mm and do not extend more than 5mm above the work piece.
Providing the tool path (center of the cutting path) is placed at least 6mm from the edge of the workpiece and the jog height is also set at 6mm, there is no possibility of the tool bit hitting a clamp. The other important factor to consider is tool bit diameter. A 3mm diameter tool bit needs a minimum of half of its diameter added to that 5mm clamp intrusion space to keep it a safe distance from the clamp. The smaller the bit diameter, the less safe distance there is so for a 3mm tool bit I add the complete diameter and a toolpath of 8mm will keep the bit far enough away from the clamp for safety.
In practice, I know that a 10mm tool path from the edge of the workpiece of any shape, will get me a safe path for the 3mm tool bit (maximum permitted on SM1) and I have no need to run a boundary. A couple of links which may assist you. (warning - there is a lot to read)
My clamp and bed system to illustrate what I have said here.
It is worth noting that CNC engineers spend a whole career learning how to accomplish the tasks they set the machines. There are a huge number of online resources but as always, at the start of any unknown journey, we do not know what it is that we must learn about. Here is a link to a useful blog that will have many articles of interest to beginners. Pick the ones you read initially and try a few general articles too. It will light the way almost without you realising it.
YouTube provides a lot of information too and you will have more than enough video presentations from which to select and watch.
For levelling the bed there are many techniques that can be used and these will frequently be machine specific but the principles will be the same across all machines. For example, if you were to put a spirit level on the bed as it is, do you know if there is any variation as you slide the spirit level from front to back or from side to side? That simple test may show you that the framework of your machine is in need of reassembly or placing on a flat and solid surface as you assemble the machine in its final position and do not move it afterwards.
The amount of cant in the spindle can also create issues if the spindle is not truly perpendicular to the bed from front to back or from side to side. There are simple techniques for straightening a canted spindle. At this point you may decide that you want (need?) to invest in a dial gauge so that you can measure these deviations accurately. The spindle may exhibit side to side deviations as it is running and this phenomenon is known as runout and can, to some extent, be cured with a dial gauge and judicious use of assembly and tightening techniques that negate sloppy manufacturing tolerances.
One quick and dirty method is to create a new wasteboard that accounts for all of the machine’s inaccuracies and has an appearance of being flat and level. So long as the machine inaccuracies do not alter, it will serve you well for wood working. Selecting the correct tool bit for the material and feeding it at the correct speed will help avoid tool bit chatter and subjecting the machine to stresses that will cause it to move out of true alignment.
The (tool)path is long and very interesting and it it will delight and frustrate you in equal measure during the coming years. There is great satisfaction to be derived from planning a project, designing it, transferring it to a machine and have the machine do exactly what you asked. Have fun with it and enjoy your successes. Laugh as you throw the failures into the trash but learn from them. Always ask yourself how your work is visiting the trash can again.
A some useful articles on end mill bits and feeding tool bits into work.
https://www.cutter-shop.com/information/chip-load-chart.html