@Chocolatebuttonns come on in.
Let's start with the crate:
~Is it small enough? If your crate is very big, then she will have plenty of space to designate a little bit as her sleeping area and the rest as her toileting area.
~I would take out her bed and replace it with a piece of vet bedding. It's quite expensive but it's so much easier to rip it out and wash it than a bed would be. I bought a fairly large piece and cut it into crate sized pieces, so that I'd have 3 pieces I could rotate in the early days.
~Did you do crate training to build up a positive association with the crate? If not, you could spend a bit of time training her to go into her crate willingly. Lure her into the crate with treats (I used kibble) and say 'Yes!' when she goes in there. Then, when she's willingly going to the crate with treats, shut the door for literally a second, then open it and give a treat. Then lure her back out of the crate with a treat, and say 'OK' as she leaves the crate. Repeat this backwards and forwards treating as she goes in and out of the crate. Gradually build up the time you shut the crate door for 3, 5, 10, 15 seconds, until you can build up to a minute or two, then 5, etc.
With toilet training, it really is about building positive association with weeing in the right place and ignoring indoor wees. So find her a place that you want her to toilet in (we put down a wooden frame with gravel and a fence around it, but you don't have to at all). Take her out on a lead - carry her there if she won't walk. Then she stays there until she's done a wee. As she does it, you can say 'Be busy' or anything else you want to use as a toilet word. Then, once she's done a wee, JACKPOT!! She gets treats, praise, cuddles, and she gets to go inside.
Toileting in the early days needs to be your very first thought - if she wakes up, toilet. Drinks...toilet. Eats...toilet. Plays...toilet. Hasn't done anything in the last 20 minutes...toilet. I personally wouldn't use puppy pads. It's confusing and gives mixed messages - you don't want her to pee indoors.
I promise it gets better. Hazel is 4 months old now, and I can't remember the last time she peed inside. When she's outside, if she needs a poo, she runs up to the gravel patch and does it before playing again.