I have never heard someone says "お疲れ様ですか". But you can say "お疲れですか" when you want to ask someone if he/she is tired politely. Also you can say "お疲れ様です"/"お疲れ様でした" when you want to say "see you tomorrow"/"take it easy"/etc to your colleague or someone, like when you are leaving the office or he/she is leaving after finishing the day business. So for your question, if you are asked "お疲れですか" by someone, you may want to say "ええ、少し"(Yes, I'm a little bit tired) or "いえ、大丈夫ですよ。"(No, I'm fine.) Or if someone say "お疲れ様" to you, you will say "お疲れ様". For "お待たせしまいました", I assume you mean "お待たせしてしまいました" or "お待たせしました" because we don't use "お待たせしまいました". "お待たせしてしまいました" is "I have made you wait" while "お待たせしました" is "I made you waited". Both expression implicitly include apologies, so it would be better say "いえ、大丈夫ですよ"(No, it's OK.) in many cases.

お疲れ様です＝ My case, actually I don't use "お疲れ様ですか？"(question style) I guess it might be used often "お疲れ様でした" when I left my office. Or "お疲れさまです", when I talk with my coworkers or a greeting to a person who work for me, such as a postman, a delivery person. If your acquaintances say "お疲れ様です"or "お疲れ様でした", you just say too "お疲れ様です！" with smiling, that's it! By the way, If you want to just ask tired or not, by question style, you should take off "様"＝"お疲れですか？" お待たせしました＝ I am not sure witch situation you want to use. I guess it's for a phone call maybe? On a phone call, I will say nothing or only say "はい" or ”いえいえ(いいえいいえ)". When shopping, I will say "いいえ、(待つことは)大丈夫ですよ" with smiling. Both, kinda greeting words such as Hello=こんにちは. When someone says こんにちは you too say こんにちは ,right? So don't worry they don't expect your perfect meaning response.