Hotel in La Paz
We stayed at Hotel Gloria ( Potosí 909) in La Paz. This was after a 4 day Salt flat jeep tour where we had extremely rustic conditions, so we were looking to "splurge" in La Paz, and hence we stayed there for about $60 per night, which is a lot for Bolivia. It has hot water, and even heat in the room during the evening. It was fine, but it was definitely a hotel, rather than a hostel type environment.
Bus from La Paz to Copacabana
We took a "local" bus to Copacabana, which was much cheaper than a tourist bus. I think a tourism package would actually pick you up at the hotel and take you there, making it really easy, but a local bus is cheap and an experience if you are interested in that. We had a taxi take us to the bus station for buses headed for Copacabana (it is somewhere different from the main bus station, but people at hotels / hostels would know). Immediately, someone was rushing us onto their bus that was leaving soon. The key thing to know for the ride is that they make you get off the bus and take a boat across some water, and you leave your bags on the bus while the bus floats across the water on a separate vessel (shown below). We were scared of doing this, but it worked out fine. Make sure you have your passport though. Another plus with the local instead of tourist bus is that all the tourist buses leave extremely early in the morning and I'm pretty sure the local buses leave throughout the day. The local bus isn't exactly comfortable, but since it's such a short ride, it's worth it for the adventure. Plus, the price difference is something like $2 vs $20.
Isla del Sol
If you're not totally comfortable with Spanish, I'd recommend hiring an English guide for touring Isla del Sol. Once again, the price difference is something like $2 for Spanish and $20 for English, but our guide had a lot of neat stories about the island that made it much more interesting. We did Isla del Sol all in one day, which is a lot of hiking but good practice for the Inca Trail. I also remember that the early morning boat ride to Isla del Sol was really cold and I was glad to have all my removable layers (hat, gloves, fleece, windbreaker, and pants). You can buy nice and warm llama wool stuff most anywhere in the Andes, but I think we saw some of the best prices in La Paz.
Lake Titicaca, Peru
For the Peru side of Lake Titicaca, we did a one day tour of the floating islands and one other island. We did not stay overnight with locals, which some people said they loved but others said was too touristy or was awkward staying with people they didn't know. Although pretty touristy, I thought the floating islands were really neat. I could have skipped going to the second island because it was a really long boat ride to get there and I thought Isla del Sol was similar but better.
While in Cusco, I highly recommend going to Pisac, which is a nearby town. There is a market there that had some of the best shopping of our entire trip, but it might not be every day of the week. It also had the 2nd best ruins I saw on the trip (Machu Picchu was #1, of course). The ruins are on on the top of a mountain next to town. Even if you hire a taxi to take you to the top, be sure to wear proper hiking clothes and bring water because it's no easy stroll. Also, be sure to bring enough money for everything because there are no ATMs in Pisac. To get to Pisac from Cusco we took a taxi to a tiny little bus station on the edge of town. Then a local bus to Pisac, which costs less than a dollar, but be sure to have small change with you. In fact, always try to have tons of small change with you because people in Bolivia and Peru really dislike making change. For food, there is a really good empanada place in one of the corners of the market. From where the bus and taxis drop off, you have to walk about a block up a street/alley to get to the market (shown below). The first section of the market you'll encounter is the produce area. If you are walking up the street towards the market, take a left as soon as you get to the produce area. Tucked away in the corner is a little courtyard with an outdoor brick oven. It's right near a hiking gear store. They also sell roasted Guinea pig there, but I'm not into that.
If you're going to see more than one of the ruins in and around Cusco, you should get a multiple day pass, which I think you can buy at any of the sites. They're a little expensive by Peru standards, so make sure you have enough cash with you for the first ruins you go to.
Try to avoid having much cash on you (or at least disperse it) when you pass from Bolivia to Peru because I've heard of a scam where they claim your money is counterfeit. Also, always have your passport in a money belt or in a safe deposit box, never in a bag. Try to get a receipt for what you put in your safe deposit box and avoid putting cash in safe deposit boxes. Also, while on non-tourist buses, never let your carry-on bags out of touch. You may even want to safety pin some of the zippers shut because I've heard a few stories of people reaching under seats (I think someone tried to do this to me in Ecuador, but my safety pins stopped them). I've never heard of problems with large bags stowed under the bus, except for them getting dirty. When we flew from the US, United gave us giant plastic bags for our hiking backpacks which we continued using whenever we checked our bags (I think most big airlines have these, but you sometimes have to ask for them). Not only did the plastic keep our bags clean, but I also thought they provided an extra layer of security just because it made it more of a pain to steal anything.