There isn't currently a way to use a custom theme without modifying the existing themes (you can choose from a small selection in Editor Profiles -> Plugin Parameters -> Code Editor), but I will add an override option in the next update, where you can add a theme.css file to a media/jce/css/codemirror/ folder to use instead of the selected theme.

Please try JCE Pro 2.9.31 Beta 2 - https://www.joomlacontenteditor.net/downloads/editor/pro/development You can now select a "Custom" option in the Code Editor Theme, and then use a codemirror.css file in media/jce/css/ to set the custom theme, for example, a theme based on Eclipse (not the use of the "cm-s-custom" selector to coincide with the "Custom" theme selection) :

.cm-s-custom span.cm-meta {color: #FF1717;}
.cm-s-custom span.cm-keyword { font-weight: bold; color: #7F0055; }
.cm-s-custom span.cm-atom {color: #219;}
.cm-s-custom span.cm-number {color: #164;}
.cm-s-custom span.cm-def {color: #00f;}
.cm-s-custom span.cm-variable {color: black;}
.cm-s-custom span.cm-variable-2 {color: #0000C0;}
.cm-s-custom span.cm-variable-3 {color: #0000C0;}
.cm-s-custom span.cm-property {color: black;}
.cm-s-custom span.cm-operator {color: black;}
.cm-s-custom span.cm-comment {color: #3F7F5F;}
.cm-s-custom span.cm-string {color: #2A00FF;}
.cm-s-custom span.cm-string-2 {color: #f50;}
.cm-s-custom span.cm-error {color: #f00;}
.cm-s-custom span.cm-qualifier {color: #555;}
.cm-s-custom span.cm-builtin {color: #30a;}
.cm-s-custom span.cm-bracket {color: #cc7;}
.cm-s-custom span.cm-tag {color: #170;}
.cm-s-custom span.cm-attribute {color: #00c;}

.CodeMirror-matchingbracket{
	border:1px solid gray;
	color:black !important;;
}
.cm-s-custom .CodeMirror-activeline-background {
    background: none repeat scroll 0 0 #e8f2ff !important;
}
.cm-s-custom .cm-matchhighlight { background: #e9e9e9 }
.cm-s-custom .cm-searching {
  background: #ffa;
  background: rgba(255, 255, 0, .4);
}

You can also edit and override any other selected theme by including the styles in the codemirror.css file.