Part X of what form?

You may need to fill out that section manually and mail the form.

Form 990

efiling is required for that amount of assets (I think the threshold is around $25 million)

ProSeries does not allow for dollar amounts greater than $1 billion in Form 990.

That would have been nice to know before I purchased the software.

Solution is to upgrade to Lacerte.

If I remember correctly, if you purchased ProSeries they let you use Lacerte on a Pay-Per-Return basis.