Dock Icons become QUESTION MARKS

i have DOCK ICONS that i have told to stay in the dock (this is how i start the programs) and every two weeks or so one or another one of these suddenly shows up as a BIG QUESTION MARK.
i asked this once before and someone said i should just drag the icon off and start the program again and make sure to tell it to stay in the dock.
but this is a major pain and makes it seem like there is something wrong with the OS not to mention it is really annoying to have to constantly re-organized my desktop.
does anyone know WHY this may happen and if so HOW to keep it from happening?
i mean, is there a PATH that gets linked to this icon and moving this data will somehow create the question mark? some other explanation?
TIA for any help.

hi kappy. again a BIG THANK YOU for helping me on this.
these are good points but there is definitely a different set of aspects to working on a mac with respect to the workflows regarding app install but i am not technically knowledgeable enough to tell you why this is so. i can just say that it is very confusing and it could use some cleaning up. just the fact that i have to post this question is an indication of this IMHO.
also, at the same time one simply has to look at all the Application folders on the mac and the various ways they are accessed or pointed to. when you say something like you just have to (manually) put the app file in the applications folder these things are all over the place.
i have an "Applications" folder under my Home folder that has two folders and one application that has installed themselves there. then i have a Dock icon that says Applications that has a list of programs, and then i have a desktop shortcut that has a list of items. if i ask myself the reasonable question of - well - HOW do i drag and drop the .app file into the Applications folder like i am supposed to, or WHERE is the Applications folder that shows all the items in my desktop shortcut or in the dock icon - - reasonable (and reasonably intelligent) people might be completely stumped.
now i /know/ that this "other" Applications folder is actually listed under my HARD DRIVE icon and not my home folder because if i double click on the desktop icon or if i open the dock icon in finder i can see that this is the case. however, this means that we are talking about something that is HIDDEN from the user on the mac OS. so for me to MANUALLY add a . app file to the Applications folder i somehow have to - well - presumably i have to make the leap of faith that when i add this file to my DESKTOP ICON i am adding it to the correct (hidden) folder and not to the one that i can see plain as day in my Home Folder but which appears to contain next to nothing.
I mean, i am manually adding an app to a desktop icon that has the same name as another folder so that it arrives in a hidden folder with the same name. this is ridiculous. this is just dumb and probably goes a long way toward adding to the confusion. the fact that the Home Folder level Application folder is the one that is visible is even dumber.
again, a set of prompts upon program installation might be a Mac OS level need and not something that should devolve down to the developers who probably have enough on their hands trying to keep up with changes in the from OS to OS.
as a concrete example on this thread - the answer my issue is that either there is no .app file in the /hidden/ Applications folder for the dock icon to continue to reference or that the ICON was added to the dock while the .app file was somewhere and now it is no longer seeing this .app file where it originally saw it.
A slightly off-topic BTW:
do you know why I have one app file in particular that i see in the Home Folder Level Applications folder?  this is a reasonably sophisticated company ostensibly they think this is a better place for the App and /they/ did this from what i can tell instead of me accidentally screwing this up because i was sleepy or distracted and not thinking about the Escheresque aspects of installing these .app files presumably? i mean, this in itself is confusing since I DO see this app icon in the dock and I DO see this app in this folder (all by its lonesome basically) but i DON'T see this app listed in my DOCK ICON list of Apps (or in my desktop shortcut list of apps) which from my perspective would/should basically cause a normal human being to think that the app is not installed...

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