Raining Cats and. . .Dogs?

Little miss Holly was fine during her first week. Now with the start of the second week, nature has added an additional concern - heavy rainfall. This morning our backyard was flooded and I made the decision to keep Holly in the kitchen for the day. I knew she would have bathroom related accidents and she did. Now I am wondering if I should have left her outside in her pen. She has her dog house, so leaving her in the pen would not have left her without shelter but I felt she might be more comfortable inside and dry. So what's the concern? Can keeping her inside interfere with her house training? Should dogs who are kenneled outside ever be penned inside? What reasons are valid to do so? Just questions to the void. . . and maybe some helpful answers.