I don't know if it's what you're looking for, but let's say you've got two patterns `foo` and `bar`, that you want to highlight in different colors.

First you need to define two highlight groups to set up the colors you want. Let's say, one with green background and the other one with blue background :

    :highlight MyGroup1 ctermbg=green guibg=green
    :highlight MyGroup2 ctermbg=blue guibg=blue

Next you need to define your two matches with the `matchadd()` function.  
For example, you could apply the green background defined in the highlight group `MyGroup1` to the pattern `foo` and the blue background defined in `MyGroup2` to the pattern `bar` :

    :call matchadd("MyGroup1", "foo")
    :call matchadd("MyGroup2", "bar")

You can access all the information (highlight group, pattern, priority, id) about your matches with the `getmatches()` function:

    :echo getmatches()

The `id` key is useful because its value allows you to delete a specific match with the `matchdelete()` function :
`:call matchdelete({id})`

Besides, if you store the output of `getmatches()` inside a variable (let's say `m`) :

    :let m = getmatches()

... then you can clear your matches with the `clearmatches()` function :

    :call clearmatches()

... and restore them with the `setmatches()` function afterwards :

    :call setmatches(m)

Finally, if you have to define those matches regularly, you can gain some time by storing the commands that define them in a separate file and source it when needed.

For example, you could store the following code in `mymatches.vim` :

    highlight MyGroup1 ctermbg=green guibg=green
    highlight MyGroup2 ctermbg=blue guibg=blue
    
    call matchadd("MyGroup1", "foo")
    call matchadd("MyGroup2", "bar")

And source it with : `:so mymatches.vim`

Note that if one of your pattern is a double quote `"`, you should escape it `"\""` or put single quotes around `'"'`.