Uploading products in bulk is possible, but you will have to make sure you insert the proper information for each of the fields in the database. This can get quite complicated if you are adding different options and categories. To bulk upload you will have to manually insert the products into the database.
The best way to get started on this is to insert some of the products manually and see how they are inserted into the database. Then you can insert the rest of the products. Since you have so many products, it is probably best that you use simple options if you are going to add options if possible. Using the simple options means that any combination of the options will not modify the price of the product.