There are some issues with the code you tried.
First, things are easier if you choose a character that shows up nowhere in your text as the delimiter for the s/// command. Alternatively, you have to escape with a \ any occurrence of the delimiter in your text.
In your first command,
sed -i -e 's/\(<span class=\"symbol\">\)\(<\/span>\)/\[/\]/\{custom-style=\"symbol\"\}/g'myfile.md
the error you get is due to the / in [/\], that is not escaped.
Also, to put a literal & in the output text, you have to escape it with a \ in your replacement expression. Otherwise & is interpreted as special and replaced with the matched portion of the pattern space.
To keep things simple, here I removed (possibly?) unnecessary escape characters and a couple of (possibly?) unneeded / (from [/\]/\{custom-style=\"symbol\"\}). I also chose | as the delimiter for the s/// command, since it does not appear in your input text. The command becomes:
sed -e 's|<span class="symbol"></span>|[\]{custom-style="symbol"}|g'
And this is what it does:
$ echo '<span class="symbol"></span>' | sed -e 's|<span class="symbol"></span>|[\]{custom-style="symbol"}|g'
[]{custom-style="symbol"}
If the string  is not static and you want to replace <span class="symbol"> with [ and </span> with ]{custom-style="symbol"} around it, whatever its value, you can use a capturing group (()) and a backreference (here, \1):
sed -e 's|<span class="symbol">\(.*\)</span>|[\1]{custom-style="symbol"}|g'
What this command does:
$ echo '<span class="symbol">whatever is here</span>' | sed -e 's|<span class="symbol">\(.*\)</span>|[\1]{custom-style="symbol"}|g'
[whatever is here]{custom-style="symbol"}
Finally, you may generally prefer to use single quotes (') instead of double quotes (") around sed scripts, to protect them from the shell - parameter expansion triggered by $, escaping effects of \...
<span ... /span>with the literal[]{custom-style="symbol"}? Why are you using two capturing groups (the\(...\))? (And I suggest you to edit your question instead of adding comments, you will make it more readable).