... circling would be a nice way to not interrupt her writing yet realize she could correct/learn those. What's a good way to learn word roots?
Yep, circling is a great idea for anything she can write on. For teaching word roots, prefixes and suffixes, I generally wing it from memory most of the time with DS5, and he knows how to use dictionary.com, but that's just a stopgap solution for now.
A Google search to get you started on finding online resources Here are some book ideas. Shop around for your best deal on books; I am using links from Amazon because the site has good cross-product links and reviews to help you:
Red Hot Root Words, Book 1:
http://www.amazon.com/dp/1593630379 (depending on her level of advancement, Book 2 may be more appropriate)
Greek and Latin Roots, Gr. 4-8:
http://www.amazon.com/dp/0881603813 (check out the similar ones on prefixes and suffixes, too)
Etymological dictionaries are also a good source, of course:
Barnhart Concise Dictionary of Etymology:
http://www.amazon.com/gp/product/0062700847Dictionary of Word Roots and Combining Forms:
http://www.amazon.com/dp/0874840538/English Words from Latin and Greek Elements (textbook):
http://www.amazon.com/dp/0816508992Oxford Pocket School Dictionary of Word Origins:
http://www.amazon.com/dp/0199111936The Oxford Dictionary of English Etymology:
http://www.amazon.com/dp/0198611129Origins: A Short Etymological Dictionary of Modern English:
http://www.amazon.com/dp/0415050774The Origins of English Words: A Discursive Dictionary of Indo-European Roots:
http://www.amazon.com/dp/0801867843 ... and, of course, the OED can be bought in both printed and software versions, the latter I believe for around $300 on CD (I have hard and software copies lying around somewhere but these days just use the web). They also offer an online subscription for an absurdly high price.