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eclipse has a built-in compiler. When developping in eclipse (or any other Java IDE), you can run from eclipse, you can package as a JAR file from eclipse, and even run a full fledged maven / gradle build from eclipse. There is no need to ever run javac by hand when you have a Java IDE.

One reason nobody in their right mind uses javac by hand is that it is notoriously picky about directories. In particular, it expects to be invoked in the root source directory, not any subdirectory thereof. So when you write:

> I compiled it from the folder that both files were inside of

you are doing it wrong. The correct file layout for Java source files looks like this:

    <source root directory>  <-- working directory for invoking javac, can have any name
      com                    <-- source files for package com
        codidact             <-- source files for package com.codidact
          software           <-- source files for package com.codidact.software
            Main.java
            Queue.java

(to avoid name conflicts, it is customary to name packages using a reversed domain name under your control, so if codidact were to write Java code, they might use the package name com.codidact.software)

In your case, that looks like this:

    <source root directory>  <-- working directory for invoking javac, can have any name
      disksim                <-- source files for package disksim
        MainClass.java
        QueueObject.java